Software

StochSS

We are pleased to announce the release of StochSS: Stochastic Simulation Service, Version 1.4. StochSS is an integrated development environment featuring state of the art algorithms for discrete stochastic biochemical simulation. StochSS is designed to enable you to easily scale up your simulations in complexity, deploying compute resources as needed. The current version includes algorithms for simulation of ODEs with sensitivity analysis, well-mixed stochastic systems , and parameter estimation for stochastic systems.

New capabilities of Version 1.4 include spatial stochastic simulation capabilities powered by the PyURDME spatial solver (http://www.pyurdme.org/).
For more details and instructions on how to obtain the code, visit us at www.StochSS.org.

Linda Petzold and Chandra Krintz
University of California Santa Barbara

Per Lotstedt and Andreas Hellander
Uppsala Universiteit

StochKit

StochKit: a Stochastic Simulation Toolbox for Biology

Other Downloads

Notes

  • DASSL and DASPK2.0 are available in the public domain.
  • DASPK3.1 is subject to copyright restrictions, but is available for research purposes. It may still be subject to revision. This latest version of DASPK3.1 includes the root-finding DAE solver DASKR (root-finding modifications to DASPK3 done by Alan Hindmarsh, LLNL). DASPKAdjoint, which uses the adjoint method for computing the sensitivity coefficients, is also included.