KaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is a static analyser for Kappa models.
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
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) - In the source directory, type
opam pin add -n .and validate - Install all the dependencies by
opam install --deps-only kappa-agents make all
If you would like to get WebSim (the Kappa REST service server), in addition of the previous steps: opam install kappa-server
Nothing worked so far. Well, you're pretty much on your own... Kappa
tools depend upon the OCaml native compiler version 4.03.0 or above as
well as dune, findlib, Lwt (>= 2.6.0), Re, Fmt, Logs and
Yojson libraries. Find any way to install them and you'll be only a
make all away from getting Kappa binaries...
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.