BioServices

BioServices is a Python package that provides access to many Bioinformatics Web Services (e.g., UniProt) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols). The package is available on Pypi repository:  BioServices

CellNetOptimizer

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

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

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

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

DrugVsDisease

DrugVsDisease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microa rray repositories.

DvD is hosted at http://www.ebi.ac.uk/saezrodriguez/DVD/