### 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

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/

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.

*posted* 2006.04.25

### XPPAUT

*posted* 2006.04.25

### FluxAnalyzer

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

*posted* 2006.04.25

### MetaboLogica

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

*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.

*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

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/

http://projects.villa-bosch.de/bcb/software/software/Ulla/SimWiz/

*posted* 2006.04.25