http://www2.unil.ch/cbg/api.php?action=feedcontributions&user=Gabor&feedformat=atomComputational Biology Group - User contributions [en]2013-05-22T23:53:25ZUser contributionsMediaWiki 1.19.1http://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2011-04-30T04:25:22Z<p>Gabor: Undo revision 2255 by Nadya (Talk)</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
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== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
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== How can I edit an existing page? ==<br />
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Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
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== Can I undo the changes I did? ==<br />
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Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
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Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
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== How can I find a page that I have already created? ==<br />
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Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
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== How can I undelete a page? ==<br />
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You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
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== How do I request a new feature? ==<br />
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Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
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== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
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== Can I change the menu on the top? ==<br />
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Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
It is pretty simple, takes two easy steps:<br />
# Create a new page, or choose the page you want to link from the title of the news entry.<br />
# Edit this page, and add the following to it (wherever you like, but maybe better at the top):<br />
<pre><br />
[[Category:Bulletins]]<br />
<teaser><br />
The message that you would like to see in the news entry comes here. It is WikiText, so it can contain links: [[ISA]]<br />
<date>15 Jul 2010 — 19:40</date><br />
</teaser><br />
</pre><br />
<br />
The <code><date>...</date></code> part is not required, and if it is not given, then the date and time of the creation of the page will be shown.<br />
<br />
If you don't want to play with the main page, then here is what you can do. Instead of the <code>Bulletins</code> category, first use the <code>BulletinsTest</code> category, and then check the top of the [[Sandbox]] page. This page shows the news entries created with the <code>BulletinsTest</code> category. If everything looks fine, then edit your page again and replace <code><nowiki>[[Category:BulletinsTest]]</nowiki></code> with <code><nowiki>[[Category:Bulletins]]</nowiki></code>.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=SandboxSandbox2011-03-31T18:46:49Z<p>Gabor: </p>
<hr />
<div><newsbulletins>header=NEWS|category=BulletinsTest</newsbulletins><br />
<br />
[[Category:BulletinsTest]]<br />
<teaser> Wow, this is a recursive news entry! <date>12 May 1898 — 12:55</date></teaser><br />
<br />
{{#css:/cbg/skins/bulletins.css}}<br />
<br />
=== This and that ===<br />
<br />
Try the time zone setting, should be around 12:13:<br />
<br />
12:13, 27 February 2009 (CET)<br />
<br />
But why doesn't it write the log times in the same time zone???<br />
<br />
=== LaTeX ===<br />
<br />
Unfortunately this is only a temporary solution:<br />
<br />
<math> \sqrt{a^2+b^2}</math><br />
<math> \sqrt{a^2+b^3}</math><br />
<br />
Within the text <math> x</math>. Hmmmm. Good. Another equation:<br />
<br />
<math> x_{1,2}=\frac{-b\pm\sqrt{b^2-4ac}}{2a}</math><br />
<br />
Hmmm.<br />
<br />
=== Biblio extension ===<br />
A citation <cite>somebook</cite>.<br />
Three citations <cite>webber2001 schwartz2005 somebook</cite>.<br />
<br />
==== References ====<br />
<biblio><br />
#schwartz2005 pmid=16100001 <br />
// see also <cite>stryer somebook</cite> for a smooth introduction<br />
#webber2001 pmid=11751224 // [[Media:foobar|PDF]] <br />
#somebook John Smith. ''The art of saying nothing''. Verbose Editions 1999.<br />
#stryer isbn=0-7167-4954-8<br />
# Arnedo2007 pmid=17700364 // [[Media:Lipogen2.pdf|PDF]]<br />
# Bergmann2007 pmid=17298180 // [[Media:Fly.pdf|PDF]]<br />
</biblio><br />
<br />
Should be ok now.<br />
<br />
Testing email address as an image: <email>xy@unil.ch</email>.<br />
<br />
Link to DGM Wiki: [[DGM:Sandbox]]<br />
<br />
=== Code highlighting ===<br />
<br />
==== LaTeX ====<br />
<br />
<source lang="latex"><br />
\documentclass{article}<br />
\begin{document}<br />
\section{Introduction}<br />
This is the first paragraph.<br />
\end{document}<br />
</source><br />
<br />
==== C ====<br />
<br />
<source lang="c"><br />
#include <stdio.h><br />
int main(void) {<br />
printf("Hello world!");<br />
return(0);<br />
}<br />
</source><br />
<br />
==== R ====<br />
<br />
<source lang="r"><br />
y <- rt(200, df = 5)<br />
qqnorm(y); qqline(y, col = 2)<br />
qqplot(y, rt(300, df = 5))<br />
</source><br />
<br />
=== HTML embedding ===<br />
<br />
<htmlet>test</htmlet><br />
<br />
=== Google Analytics (with links) ===<br />
<br />
<googa>http://google.com|Search with google|/outgoing/googlesearch</googa><br />
<br />
<googa>http://www.unil.ch/cbg/homepage/downloads/eisa_0.2.2.zip|Download the eisa R package|/download/eisa_0.2.2.zip</googa><br />
<br />
Checking...</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Sven_BergmannSven Bergmann2010-08-06T09:20:27Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<newstitle>Sven Bergmann is Associate Professor</newstitle><br />
<teaser><br />
Sven Bergmann has successfully completed his<br />
tenure-track as Assistant Professor and is Associate Professor since August<br />
2010.<br />
<date>1 Aug 2010 — 9:12</date><br />
</teaser><br />
<br />
<br />
[[File:Sven_pic.jpg|200px|thumb|left|Sven Bergmann, PI]] Sven Bergmann heads the [http://www2.unil.ch/cbg ''Computational Biology Group''] in the [http://www.unil.ch/dgm Department of Medical Genetics] at the [http://www.unil.ch University of Lausanne]. He studied theoretical particle physics with [http://www.weizmann.ac.il/home/ftnir Prof. Yosef Nir] at the [http://www.weizmann.ac.il Weizmann Institute of Science] (Israel) where he received his PhD in 2001. He then joined the laboratory of [http://barkai-serv.weizmann.ac.il/GroupPage/ Prof. Naama Barkai] in the Department of Molecular Genetics at the same institute, where he first worked as a [http://www.weizmann.ac.il/RGP_open/postdoc/Weizmann-Postdoc.html Koshland postdoctoral fellow] and later as staff scientist. His work in the field of computational biology comprised designing and applying novel algorithms for the analysis of large-scale expression data, as well as modeling of genetic networks pertaining to the development of the Drosophila embryo. He is affiliated with the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] since 2005 and a Cavaglieri Fellow since 2006. <br />
<br />
----<br />
<br />
* Address: Rue de Bugnon 27 - DGM 328 - CH-1005 Lausanne - Switzerland<br />
* Phone at work: ++41-21-692-5452<br />
* Cell phone: ++41-78-663-4980<br />
* e-mail: Sven.Bergmann_AT_unil.ch<br />
<br />
----<br />
<br />
PS: Do you know how to get ''smoothly'' from A to B? Well, you just need to minimize the functional expression<br />
<math> \tilde {\cal S}[y(x)] \equiv<br />
\int_{x_i}^{x_f} \left(\kappa[y(x)]\right)^\nu \, ds(x) =<br />
\int_{x_i}^{x_f} {|y''(x)|^\nu \over<br />
\left[1+y'(x)^2\right]^{3\nu-1 \over 2}} \,dx </math><br />
<br />
It turns out that it is possible to find analytically the most general solution <math>y(x)</math>, see this [[http://arxiv.org/PS_cache/physics/pdf/0105/0105039v1.pdf paper]] for details.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Sven_BergmannSven Bergmann2010-08-06T09:19:54Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<newstitle>Sven Bergmann is Associate Professor</newstitle><br />
<teaser><br />
Sven Bergmann has successfully completed his<br />
tenure-track as Assistant Professor and is Associate Professor since August<br />
2010.<br />
<date>1 Aug 2010 — 9:12</date><br />
</teaser><br />
<br />
<br />
[[File:Sven_pic.jpg|200px|thumb|left|Sven Bergmann, PI]] Sven Bergmann heads the [http://www2.unil.ch/cbg ''Computational Biology Group''] in the [http://www.unil.ch/dgm Department of Medical Genetics] at the [http://www.unil.ch University of Lausanne]. He studied theoretical particle physics with [http://www.weizmann.ac.il/home/ftnir Prof. Yosef Nir] at the [http://www.weizmann.ac.il Weizmann Institute of Science] (Israel) where he received his PhD in 2001. He then joined the laboratory of [http://barkai-serv.weizmann.ac.il/GroupPage/ Prof. Naama Barkai] in the Department of Molecular Genetics at the same institute, where he first worked as a [http://www.weizmann.ac.il/RGP_open/postdoc/Weizmann-Postdoc.html Koshland postdoctoral fellow] and later as staff scientist. His work in the field of computational biology comprised designing and applying novel algorithms for the analysis of large-scale expression data, as well as modeling of genetic networks pertaining to the development of the Drosophila embryo. He is affiliated with the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] since 2005 and a Cavaglieri Fellow since 2006. <br />
<br />
----<br />
<br />
* Address: Rue de Bugnon 27 - DGM 328 - CH-1005 Lausanne - Switzerland<br />
* Phone at work: ++41-21-692-5452<br />
* Cell phone: ++41-78-663-4980<br />
* e-mail: Sven.Bergmann_AT_unil.ch<br />
<br />
----<br />
<br />
PS: Do you know how to get ''smoothly'' from A to B? Well, you just need to minimize the functional expression<br />
<math> \tilde {\cal S}[y(x)] \equiv<br />
\int_{x_i}^{x_f} \left(\kappa[y(x)]\right)^\nu \, ds(x) =<br />
\int_{x_i}^{x_f} {|y''(x)|^\nu \over<br />
\left[1+y'(x)^2\right]^{3\nu-1 \over 2}} \,dx </math><br />
<br />
It turns out that it is possible to find analytically the most general solution <math>y(x)</math>, see this [[http://arxiv.org/PS_cache/physics/pdf/0105/0105039v1.pdf paper]] for details.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-08-06T09:17:32Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<newstitle>ISA application note</newstitle><br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] has been published recently in Bioinformatics, about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<date>24 Jul 2010 — 17:49</date><br />
</teaser><br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-08-06T09:16:57Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<newstitle>ExpressionView application note</newstitle><br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>29 Jul 2010 — 13:32</date><br />
</teaser><br />
<br />
[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
The Flash applet requires a Flash-enabled web browser. Please install Adobe Flash Player from the [http://get.adobe.com/flashplayer/ Adobe web site] if your browser does not have it yet.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
===[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf ExpressionView R package manual]===<br />
[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-08-06T09:02:06Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<newstitle>ExpressionView application note</newstitle><br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>29 Jul 2010 — 13:32</date><br />
</teaser><br />
<br />
[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
The Flash applet requires a Flash-enabled web browser. Please install Adobe Flash Player from the [http://get.adobe.com/flashplayer/ Adobe web site] if your browser does not have it yet.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
===[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf ExpressionView R package manual]===<br />
[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-08-06T08:57:56Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<newstitle><br />
ExpressionView application note<br />
</newstitle><br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>29 Jul 2010 — 13:32</date><br />
</teaser><br />
<br />
[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
The Flash applet requires a Flash-enabled web browser. Please install Adobe Flash Player from the [http://get.adobe.com/flashplayer/ Adobe web site] if your browser does not have it yet.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
===[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf ExpressionView R package manual]===<br />
[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-08-06T08:57:21Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>29 Jul 2010 — 13:32</date><br />
</teaser><br />
<br />
[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
The Flash applet requires a Flash-enabled web browser. Please install Adobe Flash Player from the [http://get.adobe.com/flashplayer/ Adobe web site] if your browser does not have it yet.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
===[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf ExpressionView R package manual]===<br />
[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-08-06T08:55:36Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] has been published recently in Bioinformatics, about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<date>24 Jul 2010 — 17:49</date><br />
</teaser><br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-08-06T08:54:45Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] has been published recently in Bioinformatics, about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<newstitle>ISA application note in Bioinformatics</newstitle><br />
<date>24 Jul 2010 — 17:49</date><br />
</teaser><br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionView_Application_NoteExpressionView Application Note2010-08-06T08:40:14Z<p>Gabor: Redirected page to ExpressionView</p>
<hr />
<div>#Redirect [[ExpressionView]]<br />
<br />
[[Category:BulletinsTest]]<br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>29 Jul 2010 — 13:32</date><br />
</teaser></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionView_Application_NoteExpressionView Application Note2010-08-06T08:38:39Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>29 Jul 2010 — 13:32</date><br />
</teaser><br />
<br />
#Redirect [[ExpressionView]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionView_Application_NoteExpressionView Application Note2010-08-06T08:37:29Z<p>Gabor: Created page with 'Category:BulletinsTest <teaser> We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster vi…'</p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<teaser><br />
We published [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq334 an application note] about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more &mdash; documentation, downloads, screenshots &mdash; on ExpressionView. <br />
<date>24 Jul 2010 — 17:49</date><br />
</teaser><br />
<br />
#Redirect [[ExpressionView]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Main_PageMain Page2010-08-04T10:45:38Z<p>Gabor: Adding link to "retrieving from backup"</p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
__NOTOC__<br />
<br />
<newsbulletins>header=NEWS</newsbulletins><br />
{{#css:/cbg/skins/bulletins.css}}<br />
<br />
== Welcome to the ''Computational Biology Group'' (CBG) at the ''[http://www.unil.ch/dgm/page13525.html Department of Medical Genetics]'' of the [http://www.unil.ch University of Lausanne]! ==<br />
<br />
(This ''Wiki'' supersedes our [http://serverdgm.unil.ch/bergmann/index.html previous homepage].)<br />
<br />
[[Image:CBG picture 2010.jpg|thumb|Photo by Nicolas Righetti|500px]]<br />
<br />
We have interest in various fields related to Computational Biology, which are detailed in the [[Science]] section of this wiki. Briefly, there are two main directions: We develop and apply methods for the integrative analysis of large-scale biological and clinical data. This includes ''molecular'' phenotypes like gene-expression data, as well as ''organismal'' phenotypes (ranging from patient data to growth arrays). We focus particularly on relating these phenotypes to genotypes such as "Single Nucleotide Polymorphisms" (SNPs) and "Copy Number Variants" (CNVs) measured by microarrays or next-generation sequencing. Our goal is to move towards predictive models in order to improve the diagnosis, prevention and treatment of disease. A complementary direction of research pertains to relatively small genetic networks, whose components are well-known. We collaborate closely with experts of the field to identify biological systems that can be modeled quantitatively. Our goal in developing such models is not only to give an approximate description of system, but also to obtain a better understanding of its properties. For example, regulatory networks evolved to function reliably under ever-changing environmental conditions. This notion of robustness can guide computational analysis and provide constraints on models that complement those from direct measurements of the system's output.<br />
<br />
In general, our group seeks an interdisciplinary approach, bridging the traditional gaps between physics, mathematics and biology. Our lab collaborates with experimental groups within and outside our department. In particular, due to our proximity to the CHUV we have close contacts to medical research groups and assist the analysis of clinical data.<br />
<br />
== Highlights of what's in this wiki: ==<br />
<br />
* Research<br />
** [[Robustness in Drosophila embryo patterning]]<br />
** [[WingX: Systems Biology of the Drosophila Wing]]<br />
** [[Genome Wide Association Studies]] (GWAS)<br />
** [[GWAS project]]<br />
<br />
* Projects (restricted to the CBG members)<br />
**[[Diana's thesis]]<br />
**[[Aitana's thesis]]<br />
**[[PGX]]<br />
<br />
* [[Teaching]]<br />
** [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
** [[UNIL BSc course: "Experimental design"]]<br />
** [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
** [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
** [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
** [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
** [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
** [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
** [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
** [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
** [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
** [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
* (currently imcomplete) list of group [[Publications]]<br />
<br />
* The schedule for our [[Group Meeting]] and our [[Journal Club]]<br />
<br />
* The [[Library]]<br />
<br />
* [[Conference Summaries]]<br />
<br />
* How-to guides <br />
** Running jobs on [[Vital-IT]] <br />
** [[Submitting lots of jobs locally]]<br />
** [[Packaging matlab to standalone]]<br />
** [[Retrieving files from backup]]<br />
<br />
* [[People|People at the CBG]]<br />
<br />
== General info on this wiki ==<br />
This wiki is the main instrument to centralize and archive information on and generated by the CBG. Creating new pages and editing existing content in the Wiki are restricted to CBG members, but by default the pages are world-readable. [mailto:wwwcbg@unil.ch Drop an email to the admin] if you want an account. If you are a [http://serverdgm.unil.ch/bergmann/ CBG] member (and have an account) you can find more information on this wiki by clicking on the [[Help:Contents|Help]] link that is in the menu on the left.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-07-26T08:32:51Z<p>Gabor: /* How can I add an entry to the News section on the front page? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
It is pretty simple, takes two easy steps:<br />
# Create a new page, or choose the page you want to link from the title of the news entry.<br />
# Edit this page, and add the following to it (wherever you like, but maybe better at the top):<br />
<pre><br />
[[Category:Bulletins]]<br />
<teaser><br />
The message that you would like to see in the news entry comes here. It is WikiText, so it can contain links: [[ISA]]<br />
<date>15 Jul 2010 — 19:40</date><br />
</teaser><br />
</pre><br />
<br />
The <code><date>...</date></code> part is not required, and if it is not given, then the date and time of the creation of the page will be shown.<br />
<br />
If you don't want to play with the main page, then here is what you can do. Instead of the <code>Bulletins</code> category, first use the <code>BulletinsTest</code> category, and then check the top of the [[Sandbox]] page. This page shows the news entries created with the <code>BulletinsTest</code> category. If everything looks fine, then edit your page again and replace <code><nowiki>[[Category:BulletinsTest]]</nowiki></code> with <code><nowiki>[[Category:Bulletins]]</nowiki></code>.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-07-24T15:57:36Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] has been published recently in Bioinformatics, about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<date>24 Jul 2010 — 17:49</date><br />
</teaser><br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-07-24T15:56:08Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] has been published recently in Bioinformatics, about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<date>24 Jul 2010 — 17:49</date><br />
</teaser><br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-07-24T15:50:07Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] was published in Bioinformatics about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<date>5 April 2010 — 17:49</date><br />
</teaser><br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ISAISA2010-07-24T15:49:40Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<teaser>A [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq130 new application note] was published in Bioinformatics about the '''isa''' and '''eisa''' packages and the Iterative Signature Algorithm.<br />
<date>5 April 2010 — 17:49</date><br />
</teaser><br />
<br />
[[image:expmat.png|An ISA transcription module|300px|right|link=ISA]]<br />
<br/><br />
Large sets of data, like expression profile from many samples, require<br />
analytic tools to reduce their complexity. <br />
The '''Iterative Signature Algorithm (ISA)''' was designed to reduce the<br />
complexity of very large sets of data by decomposing it into so-called<br />
"modules". In the context of gene expression data these modules consist of<br />
subsets of genes that exhibit a coherent expression profile only over a<br />
subset of microarray experiments. Genes and arrays may be attributed to<br />
multiple modules and the level of required coherence can be varied resulting<br />
in different "resolutions" of the modular mapping. Since the ISA does not<br />
rely on the computation of correlation matrices (like many other tools), it<br />
is extremely fast even for very large datasets.<br />
<br />
= Software for Gene expression data =<br />
<br />
We developed the <code>eisa</code> [http://www.r-project.org GNU R] package to facilitate the modular analysis of gene expression data. The package uses standard [http://www.bioconductor.org BioConductor] data structures and includes various visualization tools as well.<br />
<br />
=== Requirements, download and installation ===<br />
<br />
To use <code>eisa</code> you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the <code>eisa</code> package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
<code>eisa</code> depends on a number of other R packages: <code>isa2</code>, <code>Biobase</code>, <code>AnnotationDbi</code>, <code>Category</code>, <code>genefilter</code>, <code>DBI</code>. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("eisa")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/eisa.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/eisa_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/eisa_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
=== License ===<br />
<br />
The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Software for any tabular data =<br />
<br />
The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the <code>isa2</code> R package for such an analysis. <br />
<br />
=== Requirements ===<br />
<br />
No additional R package is required to install and use <code>isa2</code>. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the <code>build-essential</code> package.<br />
<br />
=== Installation ===<br />
<br />
The <code>isa2</code> package is available from [http://cran.r-project.org/ CRAN], the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in<br />
<br />
install.packages("isa2")<br />
<br />
at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.<br />
<br />
=== License ===<br />
<br />
The <code>isa2</code> package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.<br />
<br />
= Tutorials =<br />
<br />
===[[EISA tutorial|The Iterative Signature Algorithm for Gene Expression Data]]===<br />
Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.<br/><br />
[[EISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_tutorial.R R code]<br />
<br />
===[[EISA and the biclust package|ISA and the biclust package]]===<br />
The <code>biclust</code> package implements several biclustering algorithms. It is possible to convert the results of <code>biclust</code> to transcription modules and vice-versa. <br/><br />
[[EISA and the biclust package|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_biclust.R R code]<br />
<br />
===[[Tissue specific expression with the Iterative Signature Algorithm]]===<br />
[[Tissue specific expression with the Iterative Signature Algorithm|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/tissues.R R code]<br />
<br />
===[[EISA module trees|Hierarchical module trees]]===<br />
A module tree is the hierarchical modular organization of a data set.<br/><br />
[[EISA module trees|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/EISA_module_trees.R R code]<br />
<br />
===[[ISA tutorial|The Iterative Signature Algorithm]]===<br />
Tutorial for the analysis of tabular data with the <code>isa2</code> R package. <br/><br />
[[ISA tutorial|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_tutorial.R R code]<br />
<br />
===[[Running ISA in parallel]]===<br />
Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the <code>Rmpi</code> and <code>snow</code> R packages. <br/><br />
[[Running ISA in parallel|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_parallel.R R code]<br />
<br />
===[[ISA internals]]===<br />
[[ISA internals|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ISA_internals.R R code]<br />
<br />
= Matlab package =<br />
You can download it from [[Media:ISA package_v1.02.zip|here]]. It also includes the implementation of the Ping-pong algorithm <cite>Kutalik2008NB</cite>.<br />
<br />
= Papers =<br />
<br />
<biblio><br />
# Kutalik2008NB pmid=18464786 // [[Media:PPA.pdf|PDF]]<br />
# Ihmels2004 pmid=15606968 // [[Media:review.pdf|PDF]]<br />
# Ihmels2004a pmid=15044247 // [[Media:bioISA.pdf|PDF]]<br />
# Bergmann2004 pmid=14737187 // [[Media:comparative.pdf|PDF]]<br />
# Bergmann2003 pmid=12689096 //[[Media:ISA.pdf|PDF]]<br />
# Ihmels2002 pmid=12134151 // [[Media:SA.pdf|PDF]]<br />
</biblio></div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-07-24T15:40:13Z<p>Gabor: /* How can I add an entry to the News section on the front page? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
It is pretty simple, takes two easy steps:<br />
# Create a new page, or choose the page you want to link from the title of the news entry.<br />
# Edit this page, and the following to it (wherever you like, but maybe better at the top):<br />
<pre><br />
[[Category:Bulletins]]<br />
<teaser><br />
The message that you would like to see in the news entry comes here. It is WikiText, so it can contain links: [[ISA]]<br />
<date>15 Jul 2010 — 19:40</date><br />
</teaser><br />
</pre><br />
<br />
The <code><date>...</date></code> part is not required, and if it is not given, then the date and time of the creation of the page will be shown.<br />
<br />
If you don't want to play with the main page, then here is what you can do. Instead of the <code>Bulletins</code> category, first use the <code>BulletinsTest</code> category, and then check the top of the [[Sandbox]] page. This page shows the news entries created with the <code>BulletinsTest</code> category. If everything looks fine, then edit your page again and replace <code><nowiki>[[Category:BulletinsTest]]</nowiki></code> with <code><nowiki>[[Category:Bulletins]]</nowiki></code>.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=SandboxSandbox2010-07-24T13:49:15Z<p>Gabor: </p>
<hr />
<div><newsbulletins>header=NEWS|category=BulletinsTest</newsbulletins><br />
<br />
[[Category:BulletinsTest]]<br />
<teaser> Wow, this is a recursive news entry! <date>12 May 1898 — 12:55</date></teaser><br />
<br />
{{#css:/cbg/skins/bulletins.css}}<br />
<br />
=== This and that ===<br />
<br />
Try the time zone setting, should be around 12:13:<br />
<br />
12:13, 27 February 2009 (CET)<br />
<br />
But why doesn't it write the log times in the same time zone???<br />
<br />
=== LaTeX ===<br />
<br />
Unfortunately this is only a temporary solution:<br />
<br />
<math> \sqrt{a^2+b^2}</math><br />
<math> \sqrt{a^2+b^3}</math><br />
<br />
Within the text <math> x</math>. Hmmmm. Good. Another equation:<br />
<br />
<math> x_{1,2}=\frac{-b\pm\sqrt{b^2-4ac}}{2a}</math><br />
<br />
Hmmm.<br />
<br />
=== Biblio extension ===<br />
A citation <cite>somebook</cite>.<br />
Three citations <cite>webber2001 schwartz2005 somebook</cite>.<br />
<br />
==== References ====<br />
<biblio><br />
#schwartz2005 pmid=16100001 <br />
// see also <cite>stryer somebook</cite> for a smooth introduction<br />
#webber2001 pmid=11751224 // [[Media:foobar|PDF]] <br />
#somebook John Smith. ''The art of saying nothing''. Verbose Editions 1999.<br />
#stryer isbn=0-7167-4954-8<br />
</biblio><br />
<br />
Should be ok now.<br />
<br />
Testing email address as an image: <email>xy@unil.ch</email>.<br />
<br />
Link to DGM Wiki: [[DGM:Sandbox]]<br />
<br />
=== Code highlighting ===<br />
<br />
==== LaTeX ====<br />
<br />
<source lang="latex"><br />
\documentclass{article}<br />
\begin{document}<br />
\section{Introduction}<br />
This is the first paragraph.<br />
\end{document}<br />
</source><br />
<br />
==== C ====<br />
<br />
<source lang="c"><br />
#include <stdio.h><br />
int main(void) {<br />
printf("Hello world!");<br />
return(0);<br />
}<br />
</source><br />
<br />
==== R ====<br />
<br />
<source lang="r"><br />
y <- rt(200, df = 5)<br />
qqnorm(y); qqline(y, col = 2)<br />
qqplot(y, rt(300, df = 5))<br />
</source><br />
<br />
=== HTML embedding ===<br />
<br />
<htmlet>test</htmlet><br />
<br />
=== Google Analytics (with links) ===<br />
<br />
<googa>http://google.com|Search with google|/outgoing/googlesearch</googa><br />
<br />
<googa>http://www.unil.ch/cbg/homepage/downloads/eisa_0.2.2.zip|Download the eisa R package|/download/eisa_0.2.2.zip</googa><br />
<br />
Checking...</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=SandboxSandbox2010-07-24T13:49:01Z<p>Gabor: </p>
<hr />
<div><newsbulletins>header=NEWS|category=BulletinsTest</newsbulletins><br />
<br />
[[Category:BulletinsTest]]<br />
<teaser> Wow, this is a recursive news entry! <date>12 May 1898 — 12:55</teaser><br />
<br />
{{#css:/cbg/skins/bulletins.css}}<br />
<br />
=== This and that ===<br />
<br />
Try the time zone setting, should be around 12:13:<br />
<br />
12:13, 27 February 2009 (CET)<br />
<br />
But why doesn't it write the log times in the same time zone???<br />
<br />
=== LaTeX ===<br />
<br />
Unfortunately this is only a temporary solution:<br />
<br />
<math> \sqrt{a^2+b^2}</math><br />
<math> \sqrt{a^2+b^3}</math><br />
<br />
Within the text <math> x</math>. Hmmmm. Good. Another equation:<br />
<br />
<math> x_{1,2}=\frac{-b\pm\sqrt{b^2-4ac}}{2a}</math><br />
<br />
Hmmm.<br />
<br />
=== Biblio extension ===<br />
A citation <cite>somebook</cite>.<br />
Three citations <cite>webber2001 schwartz2005 somebook</cite>.<br />
<br />
==== References ====<br />
<biblio><br />
#schwartz2005 pmid=16100001 <br />
// see also <cite>stryer somebook</cite> for a smooth introduction<br />
#webber2001 pmid=11751224 // [[Media:foobar|PDF]] <br />
#somebook John Smith. ''The art of saying nothing''. Verbose Editions 1999.<br />
#stryer isbn=0-7167-4954-8<br />
</biblio><br />
<br />
Should be ok now.<br />
<br />
Testing email address as an image: <email>xy@unil.ch</email>.<br />
<br />
Link to DGM Wiki: [[DGM:Sandbox]]<br />
<br />
=== Code highlighting ===<br />
<br />
==== LaTeX ====<br />
<br />
<source lang="latex"><br />
\documentclass{article}<br />
\begin{document}<br />
\section{Introduction}<br />
This is the first paragraph.<br />
\end{document}<br />
</source><br />
<br />
==== C ====<br />
<br />
<source lang="c"><br />
#include <stdio.h><br />
int main(void) {<br />
printf("Hello world!");<br />
return(0);<br />
}<br />
</source><br />
<br />
==== R ====<br />
<br />
<source lang="r"><br />
y <- rt(200, df = 5)<br />
qqnorm(y); qqline(y, col = 2)<br />
qqplot(y, rt(300, df = 5))<br />
</source><br />
<br />
=== HTML embedding ===<br />
<br />
<htmlet>test</htmlet><br />
<br />
=== Google Analytics (with links) ===<br />
<br />
<googa>http://google.com|Search with google|/outgoing/googlesearch</googa><br />
<br />
<googa>http://www.unil.ch/cbg/homepage/downloads/eisa_0.2.2.zip|Download the eisa R package|/download/eisa_0.2.2.zip</googa><br />
<br />
Checking...</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-06-30T09:38:07Z<p>Gabor: /* How can I add an entry to the News section on the front page? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
It is pretty simple, takes two easy steps:<br />
# Create a new page, or choose the page you want to link from the title of the news entry.<br />
# Edit this page, and the following to it (wherever you like, but maybe better at the top):<br />
<pre><br />
[[Category:Bulletins]]<br />
<teaser><br />
The message that you would like to see in the news entry comes here. It is WikiText, so it can contain links: [[ISA]]<br />
</teaser><br />
</pre><br />
<br />
If you don't want to play with the main page, then here is what you can do. Instead of the <code>Bulletins</code> category, first use the <code>BulletinsTest</code> category, and then check the top of the [[Sandbox]] page. This page shows the news entries created with the <code>BulletinsTest</code> category. If everything looks fine, then edit your page again and replace <code><nowiki>[[Category:BulletinsTest]]</nowiki></code> with <code><nowiki>[[Category:Bulletins]]</nowiki></code>.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-06-30T09:37:32Z<p>Gabor: /* How can I add an entry to the News section on the front page? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
It is pretty simple, takes two easy steps:<br />
# Create a new page, or choose the page you want to link from the title of the news entry.<br />
# Edit this page, and the following to it (wherever you like, but maybe better at the top):<br />
<pre><br />
[[Category:Bulletins]]<br />
<teaser><br />
The message that you would like to see in the news entry comes here. It is WikiText, so it can contain links: [[ISA]]<br />
</teaser><br />
</pre><br />
<br />
If you don't want to play with the main page, then here is what you can do. Instead of the <code>Bulletins</code> category, first use the <code>BulletinsTest</code> category, and then check the top of the [[Sandbox]] page. This page shows the news entries created with the <code>BulletinsTest</code> category. If everything looks fine, then edit your page again and replace <code><nowiki>[[Category:BulletinsTest]]</nowiki></code> with <code><nowiki>[[Category:Bulletins]]</nowiki></code>.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-06-30T09:36:56Z<p>Gabor: /* How can I add an entry to the News section on the front page? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
It is pretty simple, takes two simple steps:<br />
# Create a new page, or choose the page you want to link from the title of the news entry.<br />
# Edit this page, and the following to it (wherever you like, but maybe better at the top):<br />
<pre><br />
[[Category:Bulletins]]<br />
<teaser><br />
The message that you would like to see in the news entry comes here. It is WikiText, so it can contain links: [[ISA]]<br />
</teaser><br />
</pre><br />
<br />
If you don't want to play with the main page, then here is what you can do. Instead of the <code>Bulletins</code> category, first use the <code>BulletinsTest</code> category, and then check the top of the [[Sandbox]] page. This page shows the news entries created with the <code>BulletinsTest</code> category. If everything looks fine, then edit your page again and replace <code><nowiki>[[Category:BulletinsTest]]</nowiki></code> with <code><nowiki>[[Category:Bulletins]]</nowiki></code>.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Sandbox2Sandbox22010-06-30T09:30:45Z<p>Gabor: </p>
<hr />
<div>[[Category:BulletinsTest]]<br />
<br />
<teaser> Another SandBox, it is just great! </teaser><br />
<br />
Main text.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=SandboxSandbox2010-06-30T09:29:43Z<p>Gabor: </p>
<hr />
<div><newsbulletins>header=NEWS|category=BulletinsTest</newsbulletins><br />
<br />
[[Category:BulletinsTest]]<br />
<teaser> Wow, this is a recursive news entry! </teaser><br />
<br />
{{#css:/cbg/skins/bulletins.css}}<br />
<br />
=== This and that ===<br />
<br />
Try the time zone setting, should be around 12:13:<br />
<br />
12:13, 27 February 2009 (CET)<br />
<br />
But why doesn't it write the log times in the same time zone???<br />
<br />
=== LaTeX ===<br />
<br />
Unfortunately this is only a temporary solution:<br />
<br />
<math> \sqrt{a^2+b^2}</math><br />
<math> \sqrt{a^2+b^3}</math><br />
<br />
Within the text <math> x</math>. Hmmmm. Good. Another equation:<br />
<br />
<math> x_{1,2}=\frac{-b\pm\sqrt{b^2-4ac}}{2a}</math><br />
<br />
Hmmm.<br />
<br />
=== Biblio extension ===<br />
A citation <cite>somebook</cite>.<br />
Three citations <cite>webber2001 schwartz2005 somebook</cite>.<br />
<br />
==== References ====<br />
<biblio><br />
#schwartz2005 pmid=16100001 <br />
// see also <cite>stryer somebook</cite> for a smooth introduction<br />
#webber2001 pmid=11751224 // [[Media:foobar|PDF]] <br />
#somebook John Smith. ''The art of saying nothing''. Verbose Editions 1999.<br />
#stryer isbn=0-7167-4954-8<br />
</biblio><br />
<br />
Should be ok now.<br />
<br />
Testing email address as an image: <email>xy@unil.ch</email>.<br />
<br />
Link to DGM Wiki: [[DGM:Sandbox]]<br />
<br />
=== Code highlighting ===<br />
<br />
==== LaTeX ====<br />
<br />
<source lang="latex"><br />
\documentclass{article}<br />
\begin{document}<br />
\section{Introduction}<br />
This is the first paragraph.<br />
\end{document}<br />
</source><br />
<br />
==== C ====<br />
<br />
<source lang="c"><br />
#include <stdio.h><br />
int main(void) {<br />
printf("Hello world!");<br />
return(0);<br />
}<br />
</source><br />
<br />
==== R ====<br />
<br />
<source lang="r"><br />
y <- rt(200, df = 5)<br />
qqnorm(y); qqline(y, col = 2)<br />
qqplot(y, rt(300, df = 5))<br />
</source><br />
<br />
=== HTML embedding ===<br />
<br />
<htmlet>test</htmlet><br />
<br />
=== Google Analytics (with links) ===<br />
<br />
<googa>http://google.com|Search with google|/outgoing/googlesearch</googa><br />
<br />
<googa>http://www.unil.ch/cbg/homepage/downloads/eisa_0.2.2.zip|Download the eisa R package|/download/eisa_0.2.2.zip</googa><br />
<br />
Checking...</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=SandboxSandbox2010-06-30T09:28:52Z<p>Gabor: </p>
<hr />
<div><newsbulletins>header=NEWS|categories=BulletinsTest</newsbulletins><br />
<br />
[[Category:BulletinsTest]]<br />
<teaser> Wow, this is a recursive news entry! </teaser><br />
<br />
{{#css:/cbg/skins/bulletins.css}}<br />
<br />
=== This and that ===<br />
<br />
Try the time zone setting, should be around 12:13:<br />
<br />
12:13, 27 February 2009 (CET)<br />
<br />
But why doesn't it write the log times in the same time zone???<br />
<br />
=== LaTeX ===<br />
<br />
Unfortunately this is only a temporary solution:<br />
<br />
<math> \sqrt{a^2+b^2}</math><br />
<math> \sqrt{a^2+b^3}</math><br />
<br />
Within the text <math> x</math>. Hmmmm. Good. Another equation:<br />
<br />
<math> x_{1,2}=\frac{-b\pm\sqrt{b^2-4ac}}{2a}</math><br />
<br />
Hmmm.<br />
<br />
=== Biblio extension ===<br />
A citation <cite>somebook</cite>.<br />
Three citations <cite>webber2001 schwartz2005 somebook</cite>.<br />
<br />
==== References ====<br />
<biblio><br />
#schwartz2005 pmid=16100001 <br />
// see also <cite>stryer somebook</cite> for a smooth introduction<br />
#webber2001 pmid=11751224 // [[Media:foobar|PDF]] <br />
#somebook John Smith. ''The art of saying nothing''. Verbose Editions 1999.<br />
#stryer isbn=0-7167-4954-8<br />
</biblio><br />
<br />
Should be ok now.<br />
<br />
Testing email address as an image: <email>xy@unil.ch</email>.<br />
<br />
Link to DGM Wiki: [[DGM:Sandbox]]<br />
<br />
=== Code highlighting ===<br />
<br />
==== LaTeX ====<br />
<br />
<source lang="latex"><br />
\documentclass{article}<br />
\begin{document}<br />
\section{Introduction}<br />
This is the first paragraph.<br />
\end{document}<br />
</source><br />
<br />
==== C ====<br />
<br />
<source lang="c"><br />
#include <stdio.h><br />
int main(void) {<br />
printf("Hello world!");<br />
return(0);<br />
}<br />
</source><br />
<br />
==== R ====<br />
<br />
<source lang="r"><br />
y <- rt(200, df = 5)<br />
qqnorm(y); qqline(y, col = 2)<br />
qqplot(y, rt(300, df = 5))<br />
</source><br />
<br />
=== HTML embedding ===<br />
<br />
<htmlet>test</htmlet><br />
<br />
=== Google Analytics (with links) ===<br />
<br />
<googa>http://google.com|Search with google|/outgoing/googlesearch</googa><br />
<br />
<googa>http://www.unil.ch/cbg/homepage/downloads/eisa_0.2.2.zip|Download the eisa R package|/download/eisa_0.2.2.zip</googa><br />
<br />
Checking...</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-06-30T09:20:40Z<p>Gabor: /* How can I ...? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
== How can I add an entry to the News section on the front page? ==<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=WikiFAQWikiFAQ2010-06-30T09:19:56Z<p>Gabor: /* How can I ...? */</p>
<hr />
<div>= Who can ... ? =<br />
<br />
== Who can read these pages? ==<br />
<br />
Everyone can read the pages in this Wiki. There is currently no possibility to create private pages as this feature was not used at all in the past and it makes the life of the Wiki admin very difficult.<br />
<br />
== Who can edit these pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
== Who can create new pages? ==<br />
<br />
Members of the CBG, more precisely anyone who has an account to the CBGWiki.<br />
<br />
= How can I ...? =<br />
<br />
== How can I create a new page? ==<br />
<br />
Type in the name of the page into the search box on the left, to see whether it already exists. If not, then click on "create this link" towards the top of the page.<br />
<br />
== How can I edit an existing page? ==<br />
<br />
Navigate to the page you want to edit and then click on the "edit" tab on the top.<br />
<br />
== Can I undo the changes I did? ==<br />
<br />
Yes, you can, all earlier versions of the pages are stored in the Wiki database. Click on the "history" tab of the page, and then on "undo" at the version you would like to go back to.<br />
<br />
== How do I write WikiText? ==<br />
<br />
Writing Wiki pages is quite simple, see the [[Wikipedia:Wikipedia:How_to_edit_a_page|help page of Wikipedia]]. Most of the things described here should work in the CBGWiki, too.<br />
<br />
== What are minor and major edits? ==<br />
<br />
A major edit is when you do substantial changes to a page, e.g. add a new paragraph to it, or change the time or place of the group meeting in the [[Group Meeting]] page. A minor edit is something small, e.g. correcting a typo, changing a word from boldface to italics. <br />
<br />
When you edit a page, you can classify your contribution as minor or major. Please consider using this option because people who "watch" a page (see next question below), may expect to be notified about substantial changes, but not about minor ones.<br />
<br />
== Can I get email notifications about page changes? ==<br />
<br />
Yes, you can, it is easy. First, you have to click on the "watch" tab on the top of the page, this adds it to your "watchlist". Second, you click on "my preferences" on the very top of any wiki page, scroll down to the "E-mail" section and turn on the appropriate checkbox. You can set up whether you want get notifications about the minor edits (see previous question).<br />
<br />
== How do I write formulas? ==<br />
<br />
You can use <math>\LaTeX</math> markup between <code><nowiki><math> ... </math></nowiki></code>. E.g. <code><nowiki><math>\sqrt{a^2+b^2}</math></nowiki></code> will be displayed as <math>\sqrt{a^2+b^2}</math>.<br />
<br />
We currently (and temporarily) use [http://www.forkosh.com/mathtex.html the web service of John Forkosh Associates, Inc.] to render the formulas, so many thanks to them.<br />
<br />
== Is there a way to cite [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] papers easily? ==<br />
<br />
The [http://openwetware.org/wiki/Wikiomics:Biblio Biblio] extension is installed in this Wiki. you can create references to papers by simply giving their PubMed ID. For example<br />
<br />
<pre><br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
</pre><br />
<br />
will be shown as:<br />
<br />
The Iterative Signature Algorithm <cite>ISA</cite>...<br />
<biblio><br />
# ISA pmid=12689096<br />
</biblio><br />
<br />
See [http://openwetware.org/wiki/Wikiomics:Biblio the Biblio homepage] for more help.<br />
<br />
== How do I upload files? ==<br />
<br />
Click on the [[Special:Upload|"Upload file"]] link on the left.<br />
<br />
== How can I find a page that I have already created? ==<br />
<br />
Type in its name into the search box on the left. Alternatively (if you cannot remember the name exactly), [[Special:AllPages|list all pages]] in the Wiki.<br />
<br />
== How can I undelete a page? ==<br />
<br />
You can't, but the admin can. [mailto:wwwcbg@unil.ch Write a mail to the admin.]<br />
<br />
== How do I request a new feature? ==<br />
<br />
Add it to the [[Feature Requests]] page, the admin will get emails about changes to this page automatically.<br />
<br />
== Where can I play around? ==<br />
<br />
In the [[Sandbox]], of course. This is a page that was created specifically for trying out things. Feel free to edit it any way you like.<br />
<br />
== Can I check how many visitors my page got? ==<br />
<br />
Sure, we use Google Analytics for that. All you need is a Google account, [mailto:wwwcbg@unil.ch write a mail to the admin] including your Google user name and then go to [http://www.google.com/analytics/ Google Analytics]. Alternatively, you can log in to Analytics with the common user name, <tt>cbg.unil@gmail.com</tt>, to view the reports.<br />
<br />
== Can I change the menu on the top? ==<br />
<br />
Unfortunately you can't. But you can [mailto:wwwcbg@unil.ch ask the admin] to do that for you.<br />
<br />
= Other issues =<br />
<br />
== Is this secure? ==<br />
<br />
No, not really. Since all transport goes over <tt>http</tt> without encryption, anyone on the same local network can steal your password. E.g. if you use your laptop to log int to the Wiki and you are connected through an open wireless network, then anyone within the range of the wireless signal can potentially steal your password. Please use a different password for the Wiki than the one(s) you normally use for other accounts.<br />
<br />
== Could we make this secure? ==<br />
<br />
No, not really. UNIL cannot (does not want to?) serve our Wiki through <tt>https</tt>.<br />
If you are outside the university, then you can use the UNIL VPN to make it somewhat more secure. Then the passwords travel unencrypted only between the UNIL VPN gateway and the UNIL web server. [http://www.unil.ch/ci/page62990.html See more info here.]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=SIB_Young_Bioinformatician_award_2010SIB Young Bioinformatician award 20102010-06-30T00:25:35Z<p>Gabor: </p>
<hr />
<div>[[Category:Bulletins]]<br />
<br />
<teaser><br />
On June 25 2010, during the 8th [BC]2 [http://www.bc2.ch/ Computational Biology Conference] in Basel, [http://www.isb-sib.ch/ SIB Swiss Institute of Bioinformatics] announced the winner of the [http://www.isb-sib.ch/research/sib-awards/sib-2010-young-bioinformatician-award.html SIB Young Bioinformatician Award 2010].<br />
<br />
The winner is SIB Member [[Aitana Morton de Lachapelle]], 27, PhD student in the Computational Biology Group led by Prof. Sven Bergmann at the Department of Medical Genetics of the University of Lausanne.<br />
</teaser><br />
<br />
On June 25 2010, during the 8th [BC]2 [http://www.bc2.ch/ Computational Biology Conference] in Basel, [http://www.isb-sib.ch/ SIB Swiss Institute of Bioinformatics] announced the winner of the [http://www.isb-sib.ch/research/sib-awards/sib-2010-young-bioinformatician-award.html SIB Young Bioinformatician Award 2010].<br />
<br />
[[Image:aitana_sib_award_2010.JPG|thumb|Aitana Morton de Lachapelle, Basel, June 25 2010|300px]]<br />
<br />
The winner is SIB Member [[Aitana Morton de Lachapelle]], 27, PhD student in the Computational Biology Group led by Prof. Sven Bergmann at the Department of Medical Genetics of the University of Lausanne, which she joined after graduating in Physics from the EPFL (Swiss Federal Institute of Technology in Lausanne). During her PhD thesis, she has been investigating how robust pattern formation can be achieved during development.<br />
<br />
Within a developing organism, cells need to know where they are in order to differentiate into the correct cell type.<br />
Pattern formation is the process by which cells acquire positional information and thus determine their fate.<br />
This can be achieved by the production and release of a diffusible signaling molecule, called a “morphogen”,<br />
which forms a concentration gradient: exposure to different morphogen levels then leads to different cell fates.<br />
Though morphogens have been known for decades, Mrs. Morton de Lachapelle explains that “it is not yet clear<br />
how these gradients form and yield such robust patterns. We have been investigating the properties of Bicoid<br />
and Decapentaplegic, two morphogens involved in the patterning of the anterior-posterior axis of Drosophila<br />
embryo and wing primordium, respectively”. In particular, she is interested in understanding how the pattern<br />
proportions are maintained across embryos of different sizes or within a growing tissue, which is essential to<br />
yield a correctly proportioned organism or organ. Ultimately, the general understanding of how cells respond to<br />
signals and coordinate their actions could bring new insights into some diseases like cancer and, theoretically,<br />
provide the ground to make artificial tissues.<br />
<br />
<br />
[[Image:aitana_sven_sib_award_2010.JPG|thumb|Aitana Morton de Lachapelle & Sven Bergmann, Basel, June 25 2010|left|400px]]<br />
<br />
In their published work, Mrs. Morton de Lachapelle and Prof. Bergmann investigated two systems properties of<br />
Drosophila early embryo development: using staining images for three gap genes and the pair-rule gene Eve,<br />
they investigated the precision and scaling of their expression domains. Their results suggest that these<br />
properties are, at least in part, already achieved at the level of the Bicoid gradient itself and then passed on to its<br />
target genes. Investigating models that can reproduce the position-dependent signatures of precision and<br />
scaling, they identified two necessary ingredients: it is essential to include nuclear trapping and an external pre-steady state morphogen gradient to achieve both maximal precision at mid-embryo and almost perfect scaling<br />
away from the source. Current work within the SystemsX.ch WingX collaboration aims at understanding how<br />
scaling can be achieved by the Decapentaplegic signaling pathway during wing imaginal disc growth.<br />
<br />
The Young Bioinformatician Award is given yearly by SIB Swiss Institute of Bioinformatics. It recognises a graduate student or young researcher who has carried out a research project centered on the in silico analysis of biological sequences, structures and processes. The award is given competitively by a jury of experts and is doted with a cash prize of CHF 10'000.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Main_PageMain Page2010-06-29T12:37:16Z<p>Gabor: </p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
__NOTOC__<br />
<br />
= NEWS! [[SIB Young Bioinformatician award 2010]] =<br />
<br />
== Welcome to the ''Computational Biology Group'' (CBG) at the ''[http://www.unil.ch/dgm/page13525.html Department of Medical Genetics]'' of the [http://www.unil.ch University of Lausanne]! ==<br />
<br />
(This ''Wiki'' supersedes our [http://serverdgm.unil.ch/bergmann/index.html previous homepage].)<br />
<br />
[[Image:CBG picture 2010.jpg|thumb|Photo by Nicolas Righetti|500px]]<br />
<br />
We have interest in various fields related to Computational Biology, which are detailed in the [[Science]] section of this wiki. Briefly, there are two main directions: We develop and apply methods for the integrative analysis of large-scale biological and clinical data. This includes ''molecular'' phenotypes like gene-expression data, as well as ''organismal'' phenotypes (ranging from patient data to growth arrays). We focus particularly on relating these phenotypes to genotypes such as "Single Nucleotide Polymorphisms" (SNPs) and "Copy Number Variants" (CNVs) measured by microarrays or next-generation sequencing. Our goal is to move towards predictive models in order to improve the diagnosis, prevention and treatment of disease. A complementary direction of research pertains to relatively small genetic networks, whose components are well-known. We collaborate closely with experts of the field to identify biological systems that can be modeled quantitatively. Our goal in developing such models is not only to give an approximate description of system, but also to obtain a better understanding of its properties. For example, regulatory networks evolved to function reliably under ever-changing environmental conditions. This notion of robustness can guide computational analysis and provide constraints on models that complement those from direct measurements of the system's output.<br />
<br />
In general, our group seeks an interdisciplinary approach, bridging the traditional gaps between physics, mathematics and biology. Our lab collaborates with experimental groups within and outside our department. In particular, due to our proximity to the CHUV we have close contacts to medical research groups and assist the analysis of clinical data.<br />
<br />
== Highlights of what's in this wiki: ==<br />
<br />
* Research<br />
** [[Robustness in Drosophila embryo patterning]]<br />
** [[WingX: Systems Biology of the Drosophila Wing]]<br />
** [[Genome Wide Association Studies]] (GWAS)<br />
** [[GWAS project]]<br />
<br />
* Projects (restricted to the CBG members)<br />
**[[Diana's thesis]]<br />
**[[Aitana's thesis]]<br />
**[[PGX]]<br />
<br />
* [[Teaching]]<br />
** [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
** [[UNIL BSc course: "Experimental design"]]<br />
** [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
** [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
** [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
** [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
** [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
** [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
** [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
** [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
** [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
** [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
* (currently imcomplete) list of group [[Publications]]<br />
<br />
* The schedule for our [[Group Meeting]] and our [[Journal Club]]<br />
<br />
* The [[Library]]<br />
<br />
* [[Conference Summaries]]<br />
<br />
* How-to guides <br />
** Running jobs on [[Vital-IT]] <br />
** [[Submitting lots of jobs locally]]<br />
** [[Packaging matlab to standalone]]<br />
<br />
* [[People|People at the CBG]]<br />
<br />
== General info on this wiki ==<br />
This wiki is the main instrument to centralize and archive information on and generated by the CBG. Creating new pages and editing existing content in the Wiki are restricted to CBG members, but by default the pages are world-readable. [mailto:wwwcbg@unil.ch Drop an email to the admin] if you want an account. If you are a [http://serverdgm.unil.ch/bergmann/ CBG] member (and have an account) you can find more information on this wiki by clicking on the [[Help:Contents|Help]] link that is in the menu on the left.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-31T09:13:22Z<p>Gabor: /* Tutorials */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
The Flash applet requires a Flash-enabled web browser. Please install Adobe Flash Player from the [http://get.adobe.com/flashplayer/ Adobe web site] if your browser does not have it yet.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
===[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf ExpressionView R package manual]===<br />
[http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T20:54:12Z<p>Gabor: /* Download the R package (includes the Flash applet) */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
The Flash applet requires a Flash-enabled web browser. Please install Adobe Flash Player from the [http://get.adobe.com/flashplayer/ Adobe web site] if your browser does not have it yet.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T20:48:10Z<p>Gabor: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The ExpressionView data file is an XML file. We have created a corresponding XML Schema file that defines its structure.<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/expressionview.xsd ExpressionView XML data file schema]<br />
<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T19:25:17Z<p>Gabor: /* Download the R package (includes the Flash applet) */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the ExpressionView package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T19:20:16Z<p>Gabor: /* Additional documentation and downloads */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T19:18:56Z<p>Gabor: /* Requirements and installation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
<br />
To use the ExpressionView R package you will need a working [http://www.r-project.org GNU R] installation. <br />
<br />
As of the 23rd of April, 2010, the ExpressionView package is an official [http://www.bioconductor.org BioConductor] package.<br />
<br />
ExpressionView depends on a number of other R packages: isa2, Biobase, AnnotationDbi, etc. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in<br />
<br />
source("http://bioconductor.org/biocLite.R")<br />
biocLite("ExpressionView")<br />
<br />
at your R prompt. See [http://bioconductor.org/packages/release/bioc/html/ExpresionView.html the eisa package page at the BioConductor website] for details.<br />
<br />
Alternatively, you can also download the package from here:<br />
<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip Microsoft Windows (32 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip Microsoft Windows (64 bit)]''' <br/>Download [http://www.unil.ch/cbg/homepage/downloads/win64/ExpressionView_1.0.0.zip this file], save it in a temporary directory, and then start R. From the Packages menu choose '<code>Install packages from local zip files</code>' and select the saved file.<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz Mac OSX (Leopard)]''' <br/> Download and install [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tgz this file].<br />
* '''[http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz Linux and Unix systems, R source package]''' <br/> Download [http://www.unil.ch/cbg/homepage/downloads/ExpressionView_1.0.0.tar.gz this file], save it in a temporary directory, and start R. Install the downloaded package using the <code>install.packages()</code> function: give the full path of the saved file and use the '<code>repos=NULL</code>' argument of <code>install.packages()</code>.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T19:08:32Z<p>Gabor: /* Documentation */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Tutorials =<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T19:05:18Z<p>Gabor: /* Tutorials */</p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Documentation =<br />
<br />
== Tutorials ==<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
[[Getting started with ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.pdf PDF]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.Rnw Rnw]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.tutorial.R R code]<br />
<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
[[Ordering algorithm used in ExpressionView|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.ordering.pdf PDF]<br />
<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
[[ExpressionView File Format|HTML]]<br />
[http://www2.unil.ch/cbg/homepage/downloads/ExpressionView.format.pdf PDF]<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T18:47:10Z<p>Gabor: </p>
<hr />
<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
<br style="clear: both" /><br />
<br><br />
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
<br />
= Demos =<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
<br />
= Requirements and installation =<br />
<br />
== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
<br />
== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
<br />
== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
<br />
= License =<br />
<br />
The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
<br />
= Documentation =<br />
<br />
== Tutorials ==<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
<br />
===[[Getting started with ExpressionView|Getting started with ExpressionView]]===<br />
===[[Ordering algorithm used in ExpressionView|Ordering algorithm used in ExpressionView]]===<br />
===[[ExpressionView File Format|ExpressionView File Format]]===<br />
<br />
=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
<br />
=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
<br />
= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
<br />
For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=EV_orderingEV ordering2010-05-26T18:46:34Z<p>Gabor: moved EV ordering to Ordering algorithm used in ExpressionView</p>
<hr />
<div>#REDIRECT [[Ordering algorithm used in ExpressionView]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Ordering_algorithm_used_in_ExpressionViewOrdering algorithm used in ExpressionView2010-05-26T18:46:34Z<p>Gabor: moved EV ordering to Ordering algorithm used in ExpressionView</p>
<hr />
<div><htmlet>ExpressionView.ordering</htmlet><br />
<br />
{{#css:/cbg/htmlets/ExpressionView.ordering.css}}</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=EV_tutorialEV tutorial2010-05-26T18:46:03Z<p>Gabor: moved EV tutorial to Getting started with ExpressionView</p>
<hr />
<div>#REDIRECT [[Getting started with ExpressionView]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Getting_started_with_ExpressionViewGetting started with ExpressionView2010-05-26T18:46:03Z<p>Gabor: moved EV tutorial to Getting started with ExpressionView</p>
<hr />
<div><htmlet>ExpressionView.tutorial</htmlet><br />
<br />
{{#css:/cbg/htmlets/ExpressionView.tutorial.css}}</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Ordering_algorithm_used_in_ExpressionViewOrdering algorithm used in ExpressionView2010-05-26T18:43:10Z<p>Gabor: Created page with '<htmlet>ExpressionView.ordering</htmlet> {{#css:/cbg/htmlets/ExpressionView.ordering.css}}'</p>
<hr />
<div><htmlet>ExpressionView.ordering</htmlet><br />
<br />
{{#css:/cbg/htmlets/ExpressionView.ordering.css}}</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Getting_started_with_ExpressionViewGetting started with ExpressionView2010-05-26T18:42:30Z<p>Gabor: Created page with '<htmlet>ExpressionView.tutorial</htmlet> {{#css:/cbg/htmlets/ExpressionView.tutorial.css}}'</p>
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<div><htmlet>ExpressionView.tutorial</htmlet><br />
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{{#css:/cbg/htmlets/ExpressionView.tutorial.css}}</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=ExpressionViewExpressionView2010-05-26T15:35:18Z<p>Gabor: </p>
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<div>[[image:Expressionview.screenshot.png|Screenshot of the ExpressionView applet|500px|left]]<br />
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ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.<br />
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= Demos =<br />
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* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.small.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (8 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html?filename=../data/Expressionview.sampledata.all.large.evf Launch ExpressionView with adult T-cell acute lymphocytic leukemia (ALL) data (108 modules)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/flash/ExpressionView.html Launch ExpressionView]<br />
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= Requirements and installation =<br />
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== Download the R package (includes the Flash applet) ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_windows.zip Windows binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_32.tar.gz Mac OS X 32 bit binary package], [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_macosx_64.tar.gz Mac OS X 64 bit binary package]<br />
* [http://www2.unil.ch/cbg/software/expressionview/r/ExpressionView_0.2.6_source.tar.gz Source package]<br />
Note that ExpressionView requires the '''[[ISA|eisa R package]]'''.<br />
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== Download the stand-alone viewer (Adobe AIR) ==<br />
If you prefer a stand-alone viewer, you can download and install the Adobe AIR build [http://www2.unil.ch/cbg/software/expressionview/air/ExpressionView.air ExpressionView.air] (right-click to download file).<br><br />
To run the program, you need the AIR runtime environment which you can get from [http://get.adobe.com/air Adobe].<br><br />
ExpressionView creates files associations to .evf files, allowing you to simply double-click on such files to launch the viewer and load the data.<br />
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== Download sample data ==<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.small.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 8 modules] (right-click to download file).<br />
* [http://www2.unil.ch/cbg/software/expressionview/data/Expressionview.sampledata.all.large.evf Gene expression profile of adult T-cell acute lymphocytic leukemia (ALL) with 108 modules] (right-click to download file).<br />
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= License =<br />
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The ExpressionView package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
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= Screenshots = <br />
<gallery widths="200px" heights="109px" perrow="3"><br />
image:Expressionview.screenshot.1.png|Startup screen<br />
image:Expressionview.screenshot.2.png|Global view after loading dataset<br />
image:Expressionview.screenshot.3.png|Highlighting modules<br />
image:Expressionview.screenshot.4.png|Zoom functions<br />
image:Expressionview.screenshot.5.png|Highlighting genes (probes) and samples<br />
image:Expressionview.screenshot.6.png|GO and KEGG associations<br />
image:Expressionview.screenshot.7.png|Modules view emphasizing the underlying gene expression data<br />
image:Expressionview.screenshot.8.png|Global view without gene expression data<br />
image:Expressionview.screenshot.9.png|Experiment description<br />
</gallery><br />
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= Documentation =<br />
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== Tutorials ==<br />
There are several tutorials describing how to use ExpressionView. The features of the R package are documented within the program. Just have a look at the ExpressionView help page after you have installed the package. Below, you can download the tutorial presenting the basic workflow and the description of the ordering algorithm. For the Flash applet, we have produced a few videos showing you how to use the program. <br />
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=== R package ===<br />
* [[Media:Expressionview.tutorial.pdf|Getting started with ExpressionView]]<br />
* [[Media:Expressionview.ordering.pdf|Ordering algorithm]]<br />
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=== Flash applet ===<br />
* [[Media:Expressionview.quickhelp.pdf|Quick help (pdf)]]<br />
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* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.getting.started.mov Getting started (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.tables.mov Using the tables (video tutorial, 6 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.modularview.mov Modular view (video tutorial, 4 minutes)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.view.mov Fullscreen feature (video tutorial, 1 minute)]<br />
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=== Installing the stand-alone version ===<br />
* [http://www2.unil.ch/cbg/software/expressionview/videos/Expressionview.videotutorial.standalone.mov Stand-alone installation (video tutorial, 2 minutes)]<br />
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= Additional documentation and downloads =<br />
The Flash applet is written in ActionScript. It is open source and can be built from the command line using the Adobe Flex SDK or more conveniently with the Adobe Flex Builder IDE. For more information, visit the [http://www.adobe.com/flex Flex website].<br />
* [http://www2.unil.ch/cbg/software/expressionview/source/ExpressionView.tar.gz ExpressionView source code (for the Flash applet)]<br />
* [http://www2.unil.ch/cbg/software/expressionview/doc ActionScript source code documentation]<br />
* [[Media:Expressionview.xmldescription.pdf|Documentation of the XML file structure]]<br />
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For the Flash applet, we have implemented components that could also be used in other applications. The most important one being the LargeBitmapData class that allows one to work with BitmapData of arbitrary size. In the [http://livedocs.adobe.com/flex/3/langref/flash/display/BitmapData.html standard BitmapData class], the maximum size for a BitmapData object is 8,192 pixels in width or height, and the total number of pixels cannot exceed 16,777,216 pixels. Note that the ResizablePanel class is no longer used in ExpressionView. <br />
* [[Media:Expressionview.largebitmapdata.tar.gz|ActionScript implementation of the LargeBitmapData class (allows to use bitmaps of arbitrary dimensions)]]<br />
* [[Media:Expressionview.resizablepanel.tar.gz|ActionScript implementation of the ResizablePanel class (a panel with open, maximize, minimize, close and resize buttons)]]</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=Main_PageMain Page2010-05-21T12:58:46Z<p>Gabor: </p>
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<div>[[Category:Homepage]]<br />
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== Welcome to the ''Computational Biology Group'' (CBG) at the ''[http://www.unil.ch/dgm/page13525.html Department of Medical Genetics]'' of the [http://www.unil.ch University of Lausanne]! ==<br />
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(This ''Wiki'' supersedes our [http://serverdgm.unil.ch/bergmann/index.html previous homepage].)<br />
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[[Image:CBG picture 2010.jpg|thumb|Photo by Nicolas Righetti|500px]]<br />
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We have interest in various fields related to Computational Biology, which are detailed in the [[Science]] section of this wiki. Briefly, there are two main directions: We develop and apply methods for the integrative analysis of large-scale biological and clinical data. This includes ''molecular'' phenotypes like gene-expression data, as well as ''organismal'' phenotypes (ranging from patient data to growth arrays). We focus particularly on relating these phenotypes to genotypes such as "Single Nucleotide Polymorphisms" (SNPs) and "Copy Number Variants" (CNVs) measured by microarrays or next-generation sequencing. Our goal is to move towards predictive models in order to improve the diagnosis, prevention and treatment of disease. A complementary direction of research pertains to relatively small genetic networks, whose components are well-known. We collaborate closely with experts of the field to identify biological systems that can be modeled quantitatively. Our goal in developing such models is not only to give an approximate description of system, but also to obtain a better understanding of its properties. For example, regulatory networks evolved to function reliably under ever-changing environmental conditions. This notion of robustness can guide computational analysis and provide constraints on models that complement those from direct measurements of the system's output.<br />
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In general, our group seeks an interdisciplinary approach, bridging the traditional gaps between physics, mathematics and biology. Our lab collaborates with experimental groups within and outside our department. In particular, due to our proximity to the CHUV we have close contacts to medical research groups and assist the analysis of clinical data.<br />
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== Highlights of what's in this wiki: ==<br />
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* Research<br />
** [[Robustness in Drosophila embryo patterning]]<br />
** [[WingX: Systems Biology of the Drosophila Wing]]<br />
** [[Genome Wide Association Studies]] (GWAS)<br />
** [[GWAS project]]<br />
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* Projects (restricted to the CBG members)<br />
**[[Diana's thesis]]<br />
**[[Aitana's thesis]]<br />
**[[PGX]]<br />
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* [[Teaching]]<br />
** [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
** [[UNIL BSc course: "Experimental design"]]<br />
** [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
** [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
** [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
** [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
** [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
** [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
** [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
** [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
** [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
** [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
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* (currently imcomplete) list of group [[Publications]]<br />
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* The schedule for our [[Group Meeting]] and our [[Journal Club]]<br />
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* The [[Library]]<br />
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* [[Conference Summaries]]<br />
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* How-to guides <br />
** Running jobs on [[Vital-IT]] <br />
** [[Submitting lots of jobs locally]]<br />
** [[Packaging matlab to standalone]]<br />
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* [[People|People at the CBG]]<br />
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== General info on this wiki ==<br />
This wiki is the main instrument to centralize and archive information on and generated by the CBG. Creating new pages and editing existing content in the Wiki are restricted to CBG members, but by default the pages are world-readable. [mailto:wwwcbg@unil.ch Drop an email to the admin] if you want an account. If you are a [http://serverdgm.unil.ch/bergmann/ CBG] member (and have an account) you can find more information on this wiki by clicking on the [[Help:Contents|Help]] link that is in the menu on the left.</div>Gaborhttp://www2.unil.ch/cbg/index.php?title=EV_formatEV format2010-05-05T19:08:35Z<p>Gabor: moved EV format to ExpressionView File Format</p>
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<div>#REDIRECT [[ExpressionView File Format]]</div>Gabor