debdaspaul / kasim

Tool suite for kappa models. Documentation and binaries can be found in the release section. Try it online at

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 as well as ocamlbuild, findlib and Yojson library. To check whether you have them, type

ocamlfind ocamlopt -version

ocamlfind query yojson

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

If you don't have any easier way to install it (opam, apt, rpm, cygwin, ...), Yojson sources are available here (Note that you'll need to compile and install also its dependencies (cppo, easy-format, biniou) from the same website).

To create binaries, simply type

make all

This should produce KaSim binaries. Ask for a data file in svg format (by giving a name ending in .svg) or you will need your own plotting program (like gnuplot) to visualize curves.

Usage

In order to run a simulation for 100 time units printing observables values every 0.5 time unit, type

bin/KaSim kappa_file_1 ... kappa_file_n -l 100 -p 0.5 -o data_file

This will produce a data file of 200 point containing the trajectory that was produced during the simulation.

Type:

bin/KaSim --help

for a complete list of options.