CellNetOptimizer (CellNOpt) is a toolbox for creating logic-based models of signal transduction networks, and training them against high-throughput biochemical data, and is freely available both for R and matlab.
CellNOpt is hosted at www.cellnopt.org
Cyrface establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller. Cyrface can be used as a Cytos cape plug-in, e.g. to run R commands within Cytoscape, or used as a library to allow your plug-in to connect to R.
Cyrface is hosted at http://www.ebi.ac.uk/saezrodriguez/cno/cyrface/
CySBGN is a Cytoscape plug-in that extends the use of Cytoscape visualization and analysis features to SBGN maps. CySBGN adds support to Cytoscape to import, export, visualize, validate and analyse SBGN maps.
CySBGN is hosted at http://www.ebi.ac.uk/saezrodriguez/cysbgn/
DataRail is an open-source MATLAB toolbox for managing, transforming, visualizing, and modeling data, in particular the high-throughput data encountered in Systems Biology.
DataRail is hosted at http://code.google.com/p/sbpipeline/wiki/DataRail