An implementation of Gillespie's stochastic simulation algorithm (SSA) with 1D diffusion
The easiest way to ensure all dependencies are met is to use a Python distribution, such as Anaconda (https://store.continuum.io/cshop/anaconda/) or Canopy (https://www.enthought.com/products/canopy/)
Specifically, this code uses:
NumPy (1.9)
Matplotlib (1.4)
PyYaml (http://pyyaml.org)
Cython (http://cython.org)
After cloning, simply run: ''' ./setup.sh '''
Make sure you add [ssa]/lib and [ssa]/src to your PYTHONPATH environmental variable, where
'[ssa]' points to the directory of the ssa code.
You may also want to add ssa/bin to your PATH
Simulations require two (YAML formatted) configuration files:
System configuration file
Defines and system and simulation run parameters:
- Run parameters (Run time, etc)
- Species definitions
- Reaction definitions
- Number of diffusion bins
Parameter configuration file
Defines parameters for the system defined in the system config file:
- Diffusion constants for each species
- Reaction rate constants
- initial species concentrations in each bin
See examples examples for more details:
sim.cfg - Simulation config
params.cfg - Parameter config
ssa_init : Preprocess configuration files and initialize simulation
ssa_run : Run or continue simulation from state file
You can use either command with option '-h' or '--help' for more information