CytoCopteR

A Cytoscape plug-in for training logic models
<http://www.cellnopt.org> Based on prior knowledge network and perturbation data, CellNOpt can derive functional information about the network using logic modeling. **CytoCopteR** is a friendly way to use CellNOpt taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge of programming languages. Version 2.0 relies on the Cyrface and CellNOptR R package. However, Version 3.x is a pure independent Java implementation. [http://msb.embopress.org/content/5/1/331.export Saez‐Rodriguez, J., Alexopoulos, L. G., Epperlein, J., Samaga, R., Lauffenburger, D. A., Klamt, S., Sorger, P. K. (2009). Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology, 5, 1. doi:10.1038/msb.2009.87] [http://www.biomedcentral.com/content/pdf/1752-0509-6-133.pdf Terfve, C., Cokelaer, T., Henriques, D., MacNamara, A., Gonçalves, E., Morris, M. K., et al. (2012). CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Systems Biology, 6, 133. doi:10.1186/1752-0509-6-133]

3.7

Works with Cytoscape 3.1

Release Notes

Fixed some bugs, see issues [https://github.com/saezlab/cytocopter/issues/2 #2], [https://github.com/saezlab/cytocopter/issues/4 #4], [https://github.com/saezlab/cytocopter/issues/5 #5] on GitHub. AND-gate expansion on multiple edges is optional from now.

3.6

Works with Cytoscape 3.1


3.5

Works with Cytoscape 3.1

Release Notes

supports SBMLqual import and export.

3.0

Works with Cytoscape 3.1

Release Notes

Version 3.x is a pure independent Java implementation. Works with Cytoscape 3.x

2.0.0

Works with Cytoscape 3.1

API   pom.xml   Javadocs


CYTOSCAPE 3

Version 3.7

Released 20 Feb 2019

Works with Cytoscape 3.1

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CYTOSCAPE 2

Version 1.2

Released 1 Aug 2013

Works with Cytoscape 2.8.3

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