Computation of logical bifurcation diagrams

The aim of this project is to be able to compute the bifurcation diagram of a given (Boolean or multivalued) logical function. To achieve this it computes the local neighbors of monotone multivalued functions.

This work is a follow-up of functionhood, with Claudine Chaouiya and José Cury, where a procedure is proposed to compute the local neighborhood of a given monotone Boolean function.

The current implementation is described in the paper submitted to Journal of Theoretical Biology, accounting only for Property 2 of the paper. Property 3 will be addressed in the future.

How to use it?

To compile it you will need Java6 JDK and maven.

• grab the source from github
• run "mvn package assembly:single" to compile and package it. Please note the assembly:single to include all the dependencies (GINsim to obtain regulators of a node and bioLQM to obtain the logical function) in the final jar package
• you can use the jar in the "target/" subdirectory.

You can either integrate the .jar file in your tool, or launch the program by command line, providing a GINsim model (.zginml file format) and the name of the component under study, as follows:

java -jar bifurcation-VERSION-jar-with-dependencies.jar model_file.zgiml ComponentName

Licence

This code is available under GPL-3.0.

Authors

Pedro T. Monteiro - ptgm

Wassim Abou-Jaoudé - aboujaoudew