SPSW 2012 summer school exercise session

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This page is about the exercise session of the SPSW 2012 summer school on Modelling Development in Plant Sciences that will take place June 21st in Mürren. The exercise session is organized by Pierre Barbier de Reuille and Micha Hersch

Contents

Summary

During the exercise session you will get introduced to Ordinary Differential Equations and how to solve them numerically using standard numerical software. We will then consider multicellular models and simulate pattern formation with Turing systems. For those already familiar with this, more advanced topics will be presented.

We will use Octave (or Matlab for those who have it) and VVE for the practicals. In order to fully benefit form the exercise session, you should install this software on your laptop and bring it to the summer school.

Installing Octave

Those who already have matlab installed don't need to install Octave. If you have troubles with the installation, write an email to Micha and he will help you.

For Windows

  1. Download this file
  2. Uncompress it (called Octave3.6.1_gcc4.6.2_20120303.7z) to some directory (let's call it octave3.6.1)
  3. Open Windows explorer and type: “octave” (without quotes) in the search box.
  4. Find the file octave.exe (or just octave) and create a short-cut to it (right-click on it and “create shortcut”)
  5. Retype “octave shortcut” in the search box
  6. Find the file “Octave.exe – Shortcut” and move it to the desktop
  7. Double click on that shortcut. A window should appear and after a while some text should appear meaning that Octave is running in it.
  8. Type: "1+1" (without quotes) in the window and check if Octave knows the answer
  9. Type: "sombrero(24)". If a nice sombrero figures appears, it means you have a working Octave installation.

For MacOS

  1. Download this dmg file
  2. Open the dmg file
  3. Open the Extras folder and the gnuplot-4-4.3-acqua-i386.dmg file inside it
  4. Put Gnuplot into the application folder
  5. .Put Octave into the Applications folder.
  6. Launch the octave application. A terminal window should appear
  7. Type: "1+1" (without quotes) in the window and check if Octave knows the answer
  8. Type: "sombrero(24)". If a nice sombrero figures appears, it means you have a working Octave installation.

If you use Lion you may have the following error: dyld: Library not loaded: /usr/X11/lib/libfreetype.6.dylib Referenced from: /usr/X11/lib/libfontconfig.1.dylib Reason: Incompatible library version: libfontconfig.1.dylib requires version 14.0.0 or later, but libfreetype.6.dylib provides version 13.0.0

The solution is the following:

Open /Applications/Gnuplot.app/Contents/Resources/bin/gnuplot in a text editor. Use the editor search-and-replace feature to replace "DYLD_LIBRARY_PATH" with "DYLD_FALLBACK_LIBRARY_PATH". There are four instances that need to be replaced.

For Linux (ubuntu)

  1. Type: “sudo apt-get install octave” (without quotes) in the command line.
  2. Type: "octave" in a terminal
  3. Type: "1+1" (without quotes) in the window and check if Octave knows the answer
  4. Type: "sombrero(24)". If a nice sombrero figures appears, it means you have a working Octave installation.

Octave basics

Those not familiar with Octave are encouraged to get acquainted with it, for example by following this tutorial

Installing VVE

For Windows

In windows, VVE is bundled into L-Studio

  1. Download L-Studio here
  2. Unzip L-Studio somewhere on your computer. The archives contains a L-Studio folder, so no need to add another one
  3. (Optional) Go into L-Studio\bin and create a symbolic link of Lstudio.exe somewhere convenient (like the desktop). You can do this with a drag&drop and pressing the Alt key when dropping.
  4. Start L-Studio by double-cliking L-Studio\bin\Lstudio.exe, or the link created in step 3
  5. You should see first a splash-screen, then a grey window entitled "L-Studio"

For Mac OS X

On Mac OS X, VVE is bundled into VLab.

  • If you have Mac OSX 10.6 (Snow Leopard):
  1. Download this dmg file for Mac OS X 10.6
  2. Copy it somewhere
  3. Launch the browser application
  4. It will ask you for a folder, which is the one where your models will be stored by default. Note that you will be able to specify this folder at every start.
  • If you have any other version of Mac OS X. you will need to compile it yourself.
  1. Download the source files
  2. contact me ( barbier -at- ips.unibe.ch )

For Linux

On Linux, VVE is bundled into VLab. Currently, you will have to contact me (barbier -at- ips.unibe.ch) to get the source code and compile it. But we should soon provide a compiled executable for Ubuntu 10.04 and 11.10.

If you have the compiled version: 1. Uncompress it somewhere

2. Go in the folder where you uncompressed it. You should have a series of folders such as "bin" and "share" 3. In the terminal, type: ./bin/postinstall.sh 4. Then, edit the file called .bashrc in your home directory (or created it if it doesn't exists, and if you are not using bash, edit the relevant configuration file) add this line in the end:

source /path/to/vlab/bin/sourceme.sh

Replacing "/path/to/vlab" with the absolute path of your vlab installation. You can obtain this if you drag&drop the folder from nautilus into your text editor.

5. Start a new shell

6. You should be able to launch the browser with "browser" in the terminal. It will ask you for a folder, which is the one where your models will be stored by default. Note that you will be able to specify this folder at every start.

If you need to compile VLab

  1. Download the source file
  2. contact me ( barbier -at- ips.unibe.ch )

Testing VVE

For Windows

  1. Uncompress this file in a folder (careful, the archive doesn't include its own folder)
  2. Start L-Studio
  3. drag-&-drop the folder where you uncompressed the file in the grey area of L-Studio
  4. You should see a text file describing the model (badly) and new menus appeared
  5. In the VVE menu, select Build
  6. In the VVE menu, select Run
  7. You should see a single green hexagon
  8. Press Ctrl-R to run the model (or use the menu). You should see cells growing and dividing with some chemical reaction forming spots

For MacOSX

  1. Download this file
  2. Start the VLab browser by starting the browser application
  3. In the browser, select a folder, then select "File->Import" and select the file you downloaded
  4. The model should appear in the folder you selected. If the folder is closed, just double-click on it
  5. Double-click on the square before the name of the model.
  6. You should see a small window appearing with some image of a tissue
  7. Right-click and select Model->Run. It can take some time as you have to compile the model
  8. Press Cmd-R to run the model (or use the menu). You should see cells growing and dividing with some chemical reaction forming spots

For Linux

  1. Download this file
  2. Start the VLab browser by typing "browser" in a terminal
  3. In the browser, select a folder, then select "File->Import" and select the file you downloaded
  4. The model should appear in the folder you selected. If the folder is closed, just double-click on it
  5. Double-click on the square before the name of the model.
  6. You should see a small window appearing with some image of a tissue
  7. Right-click and select Model->Run. It can take some time as you have to compile the model
  8. Press Ctrl-R to run the model (or use the menu). You should see cells growing and dividing with some chemical reaction forming spots