Difference between revisions of "Notebook"
 
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== 2016-07-07 ==
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*dockers: [https://github.com/rocker-org/rocker/wiki/Sharing-files-with-host-machine storing output in host]
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*DREAM dockers: setting up minimal python docker
 +
*configuring lab servers to run docker
 +
 +
== 2016-07-06 ==
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*DREAM dockers, weekly challenge call:
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** Tufts: what to dockerize, how to run
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** python code running over night
 +
 +
== 2016-07-05 ==
 +
*DREAM dockers
 +
** Read Tufts' write-up, downloaded code
 +
*Gravitating SNPs
 +
** looked at genotypes/phenotypes data
 +
 +
== 2016-06-28/29 ==
 +
* porting Roger's STOCSY code to octave: ongoing
 +
* servers' room
 +
 +
== 2016-06-26/27 ==
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*Readings:
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** PASCAL paper
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** Sven's grant
 +
 +
== 2016-06-23 ==
 +
*dockerization
 +
** Created a hello world Octave container (from Ubuntu)
 +
**[http://containertutorials.com/alpine/get_started.html Alpine]:  bash is not available.
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** [https://docs.docker.com/get-started/ Docker guide]
 +
* porting Roger's STOCSY code to octave: ongoing
 +
 +
== 2016-06-22 ==
 +
*dockerization
 +
** Created a hello world Java container (from Alpine)
 +
*Sven's research proposal: detailed research plan
 +
 +
== 2016-06-21 ==
 +
*dockerization
 +
** images vs containers: create a docker image which runs as a container
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** boot2docker if you work on a mac
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** [https://www.youtube.com/watch?v=hnxI-K10auY creating your first Dockerfile]
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*** [https://docs.docker.com/engine/reference/builder/ dockerfile]
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*** [https://docs.docker.com/samples/alpine/ Alpine] running a minimal Linux image (5MB)
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***[https://developer.atlassian.com/blog/2015/08/minimal-java-docker-containers/ minimal Java image]
 +
 +
== 2016-06-19/20 ==
 +
* Metabomatching: feature ''Import Metabolite Associations''
 +
** Added a parameter to out file: "kegg_known_x_1"
 +
**Fixed associated_snips: the tag can be repeated, the keggid must be unique.
 +
**Read loma into matrix in one go rather than iterating over each line of the file.
 +
 +
== 2016-06-12/15 ==
 +
[https://www.sib.swiss/training/upcoming-training-events/2017-06-metabolomics Metabolomics: from data to publication]
 +
 +
== 2016-06-07 ==
 +
* Preparing for SIB's "Metabolomics: from data to publication"
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** LC-MS [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/ raw data]
 +
** [https://www.quora.com/How-do-univariate-and-multivariate-statistics-differ Multivariate analysis]
 +
** In Situ Metabolomics
 +
 +
* R
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** [https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf intro]
 +
** bnlearn R package (journal club)
 +
 +
* Open-ended brainstorming with Rosanna
 +
 +
== 2016-06-06 ==
 +
* Metabomatching: adding feature ''Import Metabolite Associations''
 +
** done: waiting for code review w/ Rico
 +
 +
* Bayesian Networks: background reading for journal club
 +
 +
== 2016-06-02 ==
 +
* <code>setsid [program]</code> to fork a process
 +
 +
* Metabomatching: adding feature ''Import Metabolite Associations''
 +
**creating functions
 +
**looping through structures
 +
 
== 2016-06-01 ==
 
== 2016-06-01 ==
 +
* p-values vs. Bayes factors ''with Marco and Daniele''
 +
 
* Q-Q plots ''with Reyhan''
 
* Q-Q plots ''with Reyhan''
−
* p-values vs. Bayes factors ''with Marco and Daniele''
+
 
 
* GIT and matlab
 
* GIT and matlab
−
* From Bench to Market @ EPFL
 
  
−
== 2016-06-02 ==
+
* "From Bench to Market" @ EPFL
−
* <code>setseid [program] </code> to fork a process
 
−
* Metabomatching: adding feature ''Import Metabolite Associations''
 
−
** created function
 

Latest revision as of 12:41, 7 July 2017

2016-07-07

  • dockers: storing output in host
  • DREAM dockers: setting up minimal python docker
  • configuring lab servers to run docker

2016-07-06

  • DREAM dockers, weekly challenge call:
    • Tufts: what to dockerize, how to run
    • python code running over night

2016-07-05

  • DREAM dockers
    • Read Tufts' write-up, downloaded code
  • Gravitating SNPs
    • looked at genotypes/phenotypes data

2016-06-28/29

  • porting Roger's STOCSY code to octave: ongoing
  • servers' room

2016-06-26/27

  • Readings:
    • PASCAL paper
    • Sven's grant

2016-06-23

  • dockerization
    • Created a hello world Octave container (from Ubuntu)
    • Alpine: bash is not available.
    • Docker guide
  • porting Roger's STOCSY code to octave: ongoing

2016-06-22

  • dockerization
    • Created a hello world Java container (from Alpine)
  • Sven's research proposal: detailed research plan

2016-06-21

2016-06-19/20

  • Metabomatching: feature Import Metabolite Associations
    • Added a parameter to out file: "kegg_known_x_1"
    • Fixed associated_snips: the tag can be repeated, the keggid must be unique.
    • Read loma into matrix in one go rather than iterating over each line of the file.

2016-06-12/15

Metabolomics: from data to publication

2016-06-07

  • R
    • intro
    • bnlearn R package (journal club)
  • Open-ended brainstorming with Rosanna

2016-06-06

  • Metabomatching: adding feature Import Metabolite Associations
    • done: waiting for code review w/ Rico
  • Bayesian Networks: background reading for journal club

2016-06-02

  • setsid [program] to fork a process
  • Metabomatching: adding feature Import Metabolite Associations
    • creating functions
    • looping through structures

2016-06-01

  • p-values vs. Bayes factors with Marco and Daniele
  • Q-Q plots with Reyhan
  • GIT and matlab
  • "From Bench to Market" @ EPFL
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