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

KaSim logo

KaSim

Join the chat at https://gitter.im/Kappa-Dev/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 manual type

make doc

Installation

Released versions come with binaries for MacOS, Windows and Debian derivatives (as Ubuntu). Nightly builds of the master branch are built for these platforms by the continuous integration tools.

If you want or need your own build, install opam (the OCaml package manager) and initialize it (by issuing opam init) then simply type opam pin add --dev KaSim. This will compile all necessary dependencies as well as the current master branch of the git repository. Once that done, you'll also be able to make all from this directory too of course.

If you would like to get WebSim (the Kappa REST service server), type opam install atdgen cohttp-lwt-unix. Opam will recognize that you now have an optional dependency of KaSim with new capabilities and will recompile everything enabling them!

Nothing worked so far. Well, you're pretty much on your own... Kappa tools depend upon the OCaml native compiler version 4.02.3 or above as well as ocamlbuild, findlib, Lwt (>= 2.6.0) , Fmt, Logs and Yojson libraries. Find any way to install them and you'll be only a make all away from getting Kappa binaries...

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.