KaSim Development Homepage

A rule-based language for modeling protein interaction networks

KaSim Logo

The reference manual of the development version is available here. The stable versions are distributed as PDF with the binaries.

Jean Krivine teaching page provides matierial to start with KaSim.

Installation

To obtain KaSim/KaSa you can either use pre-compiled binaries or compile the sources for your architecture by yourself.

Use the precompiled binaries

The easiest way to use KaSim is to use pre-compiled versions available in the release section on the github repository. Download the version that corresponds to your operating system (Windows, Linux or Mac OSX) and rename the downloaded file into KaSim (or KaSa). Note that on Mac OSX or Linux, it might be necessary to give executable permissions to KaSim (and KaSa). This can be done using the shell commands: chmod u+x KaSim (and chmod u+x KaSa).

To test whether your program does work, simply type ./KaSim \dd version on a terminal, from the directory that contains the binaries. If the version is displayed it means that the binaries are indeed compatible with your OS. Otherwise you may need to compile KaSim from the sources (see below).

Compile from the sources

Building a kappa model

Under Linux, we recommend using the GNU Emacs text editor because it has a Kappa mode that you can install.

Under Windows, there is a simple syntax highlighter for the Notepad++ text editor. It looks like this:

Sample of Notepad++ highlighter.

To install, just download the highlighter .xml file, then go to Notepad++'s Language Menu -> DefineYourLanguage -> Import, and select the file you just downloaded.

In any case, you will need Graphviz or any graph vizualizator that understands the dot format to draw generated graphs.

Pretty printing Kappa code in LaTeX

For pretty LaTeX printing, there is a language definition for the listings package available here, with a demo texfile here.

Joining the discussion

A google group of Kappa users is there to handle communication between us.

Fix

Please report any issue.

Interact at low level

You could use KaSim as an OCaml library. The detail of the API is online.

KaSim can be turned into a REST service. Here is a description of the HTTP commands.

Old material

Harvard Medical School Inria
CNRS
ENS Lyon ENS
Université Paris Diderot