Installing the Plugin
To install the plugin, download the
GIProPlugin JAR file above and save the file to
the ‘plugins’ subdirectory of your Cytoscape installation.
System Requirements
- Cytoscape 2.8.1 or newer
- 2GB of RAM
- 100MB of Disk space
Java’s default memory should be increased with vm arguments when using
this plug-in, unless small datasets are being used.
See here
for more information on how to increase Cytoscape memory
What's in the Example Data?
Four files are included in the Example data package. These example data
files are all derived from published work (see below for details of the
sources) and are provided here solely for the purpose of illustrating
the capability of GIPro. The completeness of these datasets is not guaranteed
and thus may not be suitable for biologically meaningful analysis.
- Example_PPI.txt
- Collins, S. R., Kemmeren, P., Zhao, X. C., Greenblatt, J. F., Spencer, F., Holstege, F. C., Weissman, J. S., and Krogan, N. J. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439–450
- Example_Complex.txt
- Pu, S., Vlasblom, J., Emili, A., Greenblatt, J., and Wodak, S. J. (2007) Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics 7, 944–960
- Example_GI.txt
- Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M et al (2010) The genetic landscape of a cell. Science 327: 425-431
- Orf_name_map_2010.txt
- A yeast ORF to gene name map derived from the SDG database.
