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Command line stochastic simulator for kappa models. Documentation and binaries can be found in the release section below. http://kappalanguage.org/
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README.md

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KaSim

KaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is a static analyser for Kappa models.

User manual

The reference manual is available online in pdf and html;

The latex sources are available in the man/ directory. To compile the manuel, in addition of a decent LaTeX distribution you need gnuplot and graphviz to generate images (make sure that dot is in the PATH of your OS). To generate the pdf of the manuel type

make doc

Installation

To compile KaSim, you need the OCaml native compiler version 4.02.3 or above and the findib library. To check whether you have them, type

ocamlfind ocamlopt -version

If you use a package manager (or opam, the OCaml package manager), OCaml compilers and findlib are really likely provided by it. Else, OCaml native compilers can be downloaded on INRIA's website. The Windows bundle contains findlib. Findlib sources are available on camlcity.org.

To create KaSim binaries, simply type

make bin/KaSim

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

bin/KaSim kappa_file_1 ... kappa_file_n -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:

bin/KaSim --help

for a complete list of options.

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