KaSim 4.1.2 – Stochastic Simulator for Rule-based Model

KaSim 4.1.2

:: 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

Jean Krivine

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • caml

:: DOWNLOAD

KaSim

:: MORE INFORMATION

PyBioNetFit v1.1.2 – Fitting tool for Rule-based Models

PyBioNetFit v1.1.2

:: DESCRIPTION

BioNetFit is a general-purpose fitting program for rule-based models that is compatible with BioNetGen and NFsim

::DEVELOPER

BioNetFit team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 BioNetFit

:: MORE INFORMATION

Citation

BioNetFit: a fitting tool compatible with BioNetGen, NFsim, and distributed computing environments.
Thomas BR, Chylek LA, Colvin J, Sirimulla S, Clayton AH, Hlavacek WS, Posner RG.
Bioinformatics. 2015 Nov 9. pii: btv655.