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]

3.0

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 3.0

Released 29 Nov 2016

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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