:: DESCRIPTION
KaSim is a stochastic simulator for rule-based models written in Kappa.Basically KaSim takes one or several kappa files as input and generates stochastic trajectories of various observables. KaSim implements Danos and Krivine’s network free simulation algorithm that adapts Gillespie’s algorithm for rule-based models.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.It was designed to enable a researcher to simulate the behavior of intracellular signaling systems over time and in response to defined perturbations. The outcomes of the simulations can then be tested experimentally. A unique feature of Moleculizer is that it generates species and reactions, as they are needed. This ‘on- the-fly’ mode saves time by increasing computational speed and reducing manual input by the researcher. Moleculizer uses Monte Carlo methods to simulate the reactions. Moleculizer models can be exported as SBML files that can be subsequently imported into other modeling and simulation software such as ECell.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Moleculizer is available to the public under the Lesser GNU Public License.
References:
Lok, L and Brent, R. Automatic generation of cellular reaction networks with Moleculizer 1.0. Nature Biotechnology, 1:131-136 (2005).
:: DESCRIPTION
STOCHSIM is a stochastic simulator for (bio)chemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. In STOCHSIM simple two-dimensional spatial structures have been implemented, in which nearest-neighbour interactions of molecules can be simulated.
STOCHSIM provides a general purpose biochemical simulator in which individual molecules or molecular complexes are represented as individual software objects. Reactions between molecules occur stochastically, according to probabilities derived from known rate constants. An important feature of the program is its ability to represent multiple post-translational modifications and conformational states of protein molecules.
::DEVELOPER
Bray Group: Computer Models of Bacterial Chemotaxis
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Complementary information about the program is available on the website of Nicolas Le Novère .
