SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives.
Additionally the package includes basic stochastic simulation algorithms. The package includes several example networks which can be easily modified for other networks.

Serial and parallel MPI implementations can be built and called from the command line. The serial implementation of the package can also be called from Matlab via the MEX interface with limited functionality. It supports many user specified options, including the use of antithetic sampling that can be used in some cases to increase efficiency.

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Categories

Modeling, Simulations

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Additional Project Details

Intended Audience

Science/Research, Engineering

User Interface

Command-line

Programming Language

C

Registered

2012-07-18