| 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 |
