A portal site for systems biology.

BioSens is a sensitivity analysis toolkit developed by Frank Doyle Lab. at UCSB.
http://www.chemengr.ucsb.edu/%7Eceweb/faculty/doyle/biosens/BioSens.htm

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

http://www.cytoscape.org/

A bifurcation analysis tool.
http://www.math.pitt.edu/%7Ebard/xpp/xpp.html

FluxAnalyzer is a package for the widely used commercial program MATLAB ® (Mathworks, Inc.) and provides a comprehensive and user-friendly environment facilitating stoichiometric analyses of arbitrary stoichiometric, in particular metabolic networks.

http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer

MetaboLogica is for Metabolic Data Visualization, Metabolic Flux Analysis & NMR /GC-MS experiment design.

http://www.metabologica.com/

MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way, which allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies.

http://mbel.kaist.ac.kr/mfn/

SCIpath (formerly known as MicroCore) is a pluggable suite of programs specifically designed for the analysis of microarray data.
http://www.ucl.ac.uk/oncology/MicroCore/microcore.htm

SimWiz is a collection of Java tools that aims at visualizing data resulting from different kinds of biochemical simulation processes.
http://projects.villa-bosch.de/bcb/software/software/Ulla/SimWiz/