StochSS 1.5 Available for Download!

StochSS 1.5 is now officially released!
Version 1.5 includes:

  • A new model editor: Edit models faster and easier!
  • Cost analysis functionality: Measure the cost of running jobs in the cloud
  • Cloud data reproduction: Delete cloud data and reproduce it only when it is needed
  • Cloud instance type selection: Configure what instance types are used for cloud computation

Details and instructions on how to obtain the code can be found on the Download page
Tutorials are available on the Documentation page
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lötstedt and Andreas Hellander – Uppsala University

StochSS 1.4 available for download!

We are excited to announce the release of StochSS 1.4
Version 1.4 includes spatial stochastic simulation capabilities powered by the PyURDME spatial solver (http://www.pyurdme.org/).
Details and instructions on how to obtain the code can be found on the Download page
Tutorials are available on the Documentation page
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lotstedt and Andreas Hellander – Uppsala Universiteit

Bug fixed in StochSS 1.3

A critical bug in the 1.3 StochSS binaries was fixed today which prevented Concentration to Population model conversion from working correctly. If you experienced problems with this, try a new copy of StochSS.

StochSS 1.3 available for download!

We are excited to announce the release of StochSS 1.3
Version 1.3 includes a new parameter estimation tool for stochastic biochemical systems via the Monte Carlo expectation-maximization with Modified Cross-Entropy method (MCEM2)
Details and instructions on how to obtain the code can be found on the Download page
Tutorials are available on the Documentation page
www.StochSS.org
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lotstedt and Andreas Hellander – Uppsala Universiteit

PyURDME 1.0 released !

Two members of the StochSS team, Brian Drawert and Andreas Hellander, have just released the first version of their spatial stochastic simulation software called PyURDME.
PyURDME 1.0 is a general software framework for modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral (3D) and triangular (2D) meshes. Unstructured meshes allow for a more flexible handling of complex geometries compared to structured, Cartesian meshes. The current core simulation algorithm is based on the mesoscopic reaction-diffusion master equation (RDME) model.
We plan to integrate PyURDME into StochSS soon !
 

StochSS 1.2 is now available for download!

We are excited to announce the release of StochSS:
Stochastic Simulation Service, Version 1.2.
New capabilities of Version 1.2 include: new login/authentication system, sensitivity analysis for ODE models, data import/export and enhanced plotting capabilities.
Details and instructions on how to obtain the code can be found on the Download page.
www.StochSS.org
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lotstedt and Andreas Hellander – Uppsala Universiteit

StochSS 1.1.0 is available for download!

We are excited to announce the release of StochSS:                                              Stochastic Simulation Service, Version 1.1.

New capabilities of Version 1.1 include: simulation of ODE models, tools for converting ODE models into stochastic models, support for Windows systems, and enhanced management of cloud computing resources.

Details and instructions on how to obtain the code can be found on the Download page.
www.StochSS.org
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lotstedt and Andreas Hellander – Uppsala Universiteit