Modeling and data analysis in biology

SBMLSystems Biology Markup Language is a computer-readable format for representing models of biochemical reaction networks
Virtual CellModeling and simulation framework
CopasiComplex Pathway Simulator
the little blanguage for shared models built from reusable parts
Bioinformatics ServicesComputational tools for biological complexity; services and resources for modeling and computational Biology
BioNetGenrule-based simulation of biological systems
DynaFitanalysis of (bio)chemical kinetics and equilibria
PottersWheel (alt) Systems Biology Matlab toolbox for modeling, analysis, and multi-experiment fitting
SBMLToolboxSBML import into MATLAB
Systems Biology Toolbox for MATLAB  
CellSim package for modeling networks within both arbitrary shaped heterogeneous, multi-compartment cells or homogeneous cells
cellML an open XML-based language, includes information about the model structure, mathematics, and metadata.
MATLAB SimBiologygraphical model building, simulation, and analysis
E-Cellproject in computational biology with the grand aim of whole cell simulation
GNU MCSim simulation package, written in C, which allows you to: design your own statistical or simulation models (eventually dynamic, via ODEs), perform Monte Carlo stochastic simulations, Bayesian inference through Markov Chain Monte Carlo simulations.

Regression analysis and optimization

MATLAB Optimization Toolboxsmall and large scale optimization algorithms
MATLAB Curve Fitting ToolboxGUI and functions for data analysis


AnIML analytical information markup language
UnitsML Units Markup Language is a project underway at the National Institute of Standards and Technology (NIST) to develop a schema for encoding scientific units of measure in XML. Furthermore, a database (UnitsDB) containing extensive information about scientific units is under development.
Apache Xerces robust, full-featured, commercial-quality, and freely available XML parsers
SAXON XSLT and XQuery processor, developed by Michael Kay


Open Source Initiative (OSI) Open Source Initiative (OSI), non-profit corporation dedicated to managing and promoting the Open Source Definition for the good of the community, specifically through the OSI Certified Open Source Software certification mark and program
Boost free peer-reviewed portable C++ source libraries
Subversion an open source version control system
TortoiseSVN a Subversion client, implemented as a windows shell extension
Inkscape Open Source vector graphics editor, with capabilities similar to Illustrator, CorelDraw, or Xara X, using the W3C standard Scalable Vector Graphics (SVG) file format


Teaching Modules for Cell Biology Development site for teaching modules on quantitative and computational cell biology


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