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Analysis

PyDSTool

PyDSTool is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological applications, among others.

http://pydstool.sf.net

posted 2012.03.15

GNU MCSim

GNU MCSim is a free simulation package which allows you to design your own statistical or simulation models, and perform Bayesian inference through Markov Chain Monte Carlo simulations. Starting with version 5.3.0, GNU MCSIm can import and simulate SBML models.

http://www.gnu.org/software/mcsim/

posted 2009.01.15

BioSens (UCSB)

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

posted 2006.04.25

Cytoscape

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/

posted 2006.04.25

XPPAUT

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

posted 2006.04.25

FluxAnalyzer

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

posted 2006.04.25

MetaboLogica

MetaboLogica is for Metabolic Data Visualization, Metabolic Flux Analysis & NMR /GC-MS experiment design.
http://www.metabologica.com/

posted 2006.04.25

MetaFluxNet

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/

posted 2006.04.25

SCIpath

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

posted 2006.04.25

SimWiz

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/

posted 2006.04.25