- BioSpice, Berkeley BioSpice Network Representation and Modeling System (NRMS)
- Copasi, Mendes group at VBI and Kummer group at EML Research
- Dizzy, Bolouri Group, Institute for Systems Biology, Seattle
- E-Cell, Institute for Advanced Biosciences, Keio University
- MCell, Salk Institute and Pittsburgh Supercomputing Center
- SBML, XML-based representation language for biochemical network models
- STOCKS, by Kierzek group at SysBio.pl.
- The Silicon Cell, BioCentrum Amsterdam, CWI, University of Amsterdam
- Virtual Cell, National Resource for Cell Analysis and Modeling,
NRCAM
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