| SBML | Systems Biology Markup Language is a computer-readable format for representing models of biochemical reaction networks |
| Virtual Cell | Modeling and simulation framework |
| Copasi | Complex Pathway Simulator |
| the little b | language for shared models built from reusable parts |
| Bioinformatics Services | Computational tools for biological complexity; services and resources for modeling and computational Biology |
| BioNetGen | rule-based simulation of biological systems |
| DynaFit | analysis of (bio)chemical kinetics and equilibria |
| PottersWheel (alt) | Systems Biology Matlab toolbox for modeling, analysis, and multi-experiment fitting |
| SBMLToolbox | SBML 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 SimBiology | graphical model building, simulation, and analysis |
| E-Cell | project 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. |
| MATLAB Optimization Toolbox | small and large scale optimization algorithms |
| MATLAB Curve Fitting Toolbox | GUI 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), 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 |
| free peer-reviewed portable C++ source libraries |
| Subversion | an open source version control system |
| TortoiseSVN | a Subversion client, implemented as a windows shell extension |
| 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 |
