alejob/piska

Command line stochastic simulator for spatial kappa models. Based on KaSim

# KaSim

KaSim is a stochastic simulator for rule-based models written in Kappa. A pdf of the reference manual is available here; the latex sources are available in the man/ directory.

Installation

To install you need the ocaml native compiler. To check whether you have it, type

ocamlopt.opt -version

Ocaml native compilers can be downloaded on INRIA's website. To create kaSim binaries, simply type

make

This should produce KaSim binaries. You will need your own plotting program (like gnuplot) to visualize curves.

Usage

In order to run a simulation of 1000 rule applications, type

KaSim -i kappa_file -e 1000 -p 1000 -o data_file

This will produce a data file of 1000 point (-p option) containing the trajectory that was produced during the simulation.

Type:

KaSim --help

for a complete list of options.