This page contains instructions for the installation and download of software and data files for the Systems Biology module. I will try to be both clear and brief but should questions arise, please contact me (workman AT cbs.dtu.dk).
Please download and install Cytoscape using the install bundle that matches your machine's operating system from the links below. You should not need administrator rights on your system if you select to install in your user documents (user files, directory space).
WHEN YOU ARE NOT AN ADMINISTRATOR OF YOUR COMPUTER install Cytoscape in your user directory space. How to do this: When you are going through the installation wizard, there will be a "Destination directory" option for your installation directory (where all the files are to be written). Please input or browse to your home directory which will be something like "C:\Documents and Settings\YOU\My Documents" which will instruct the installer to install the program and all its files there.
This should generate the directory,
C:\Documents and Settings\YOU\My Documents\Cytoscape_v2.6.2\go there and double-click the Cytoscape.exe file to launch Cytoscape. I recommend that you now close Cytoscape before you install the plugins.
| Cytoscape (Windows) | download |
| Cytoscape (Mac OS X) | download |
| Cytoscape (Linux/UNIX) | download |
Save or unpack the plugin files in your Cytoscape installation's "plugins" directory. Which is probably somewhere like,
C:\Program Files\Cytoscape_v2.6.2\pluginsor this if you are fortunate enough to have a Mac,
/Applications/Cytoscape_v2.6.2/plugins
| Analysis Plugins | ||
|---|---|---|
| Plugin name | link | instructions |
| NetworkAnalyzer | download | Unzip and place all "jar" files in your Cytoscape plugins directory (not just the folder) |
| MCODE | download | then place this "jar" file in your Cytoscape plugins directory |
| jActiveModules | download | then place this "jar" file in your Cytoscape plugins directory |
Download and place these files in a directory you can easily find when performing the exercise for this course. When you save the data files to your computer (e.g. on the desktop) and make sure that a ".txt" has not been added to the end of your file name. If so, remove it such that the file name ends in ".sif", or ".tab", etc.
| Data files | ||
|---|---|---|
| Name | Link | Contents |
| RUAL.subset.sif | download | Human protein-protein interactions, subset of Rual et al. |
| RUAL.subset.names.tab | download | Node attributes (gene names) for RUAL.subset network |
| galFiltered.sif | download | Yeast interaction network focusing on the regulation of galactose utilization. |
| galExpData.pvals | download | Expression matrix for Gal network (node attributes). Contains both log-ratios and p-values. |
| ORF2gene.na | download | Gene names for Gal network (node attributes) |
Once you have "installed" your plugins, make sure to restart Cytoscape if you did not close it as I recommended. If things are as they should be, your Cytoscape plugin menu should look like this, (when your mouse is over "Network Analysis" that is...)
