StochPy Files

Welcome to StochPy 2.0.1 (July 2014)

The most important improvements of StochPy 2.0 are listed here:
- delayed stochastic algorithms
- volume dependency
- completely new cell division module

StochPy is a versatile modeling package for stochastic simulation of molecular control networks inside living cells. Its integration with Python’s scientific libraries and PySCeS makes it an easily extensible and an user-friendly simulator. The high-level statistical and plotting functions of StochPy allow for quick and interactive model interrogation at the command-line. Python’s scripting capabilities allow for more complicated and in-depth analysis of stochastic models. 

Because of the flexible design of StochPy, we decided to offer users of StochPy both the Cain and StochKit stochastic solvers in StochPy. As a result, the user can benefit from the speed advantage of these fixed-interval solvers in the interactive modeling environment of StochPy. StochPy's solvers return the original stochastic simulation output which makes it slower than these fixed-interval solvers. However, the original data allows us to store all the data of the simulation such that we can analyze the information about the time between events (waiting times). 

For fixed-interval simulations note that the number of fixed-interval chosen by the user determines the accuracy of the simulation results. As an example, creating accurate probability density functions requires a number of fixed-intervals that is in the same order of the number of time steps. On the other hand, frame-based simulations can be useful to get an indication of the behavior of your model, or to get the species means and standard deviations in a faster manner.

This version of StochPy allows users to specify which species have to be tracked over time, which can result in a major reduction of stored data for models with many species. Alternatively, StochPy now offers an option to store only the last time point of a simulation.

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