Links
Stochastic Simulations.
-
The SBML (Systems Biology Markup Language)
homepage has links to many software projects.
-
Linda Petzold and her research group at
UCSB
(including Hong Li,
Kevin Sanft,
Min Roh,
and
Brian Drawert)
study stochastic simulation methods and have developed
StochKit.
-
Darren Wilkinson,
provides software and test models at his web site.
-
DSMTS
(Discrete Stochastic Models Test Suite) is a test suite in SBML format.
-
Dizzy
is a chemical kinetics stochastic simulation software package written in
Java.
-
COPASI
is a software application for simulation and analysis of biochemical networks.
-
FERN
(Framework for Evaluation of Reaction Networks) is an extensible and
comprehensive framework for efficient simulations and analysis of chemical
reaction networks written in Java.
-
CellMC
is an open source program generator that compiles a mesoscopic model of a
biochemical reaction network, expressed as SBML, into an executable program
that realizes SSA for that model; the program can then be run for any final
simulation time and number of realizations.
-
STOCKS
is public domain (GNU GPL) software for stochastic simulations of
biochemical processes.
-
SimBiology
provides graphical and programmatic tools for modeling, simulating, and
analyzing biological systems.
Open-source software resources.
-
SourceForge hosts a wealth of
software projects.
-
freshmeat maintains the Web's largest
index of Unix and cross-platform software.
Software.