A multilevel to Boolean gene regulatory network converter
- @author Shizuo KAJI
- @date 20 Jan. 2017
- @date updated on 24 Mar. 2017
- @copyright The MIT License
A perl script to convert multilevel networks to Boolean networks
The algorithm is based on the paper "A circuit-preserving mapping from multilevel to Boolean dynamics" by A. Faure and S. Kaji and "On the conversion of multivalued gene regulatory networks to Boolean dynamics" by E. Tonello, arXiv:1703.06746
How to use:
- Define your model in the "Truth Table" (tt) format. (GINSim can read and write tt files)
- For the Faure-Kaji algorithm perl multi2boolean.pl example.tt > out.tt
- For the Tonello algorithm perl multi2boolean.pl -t example.tt > out.tt
- the resulting out.tt is again in the Truth Table format.
Truth Table (tt) format:
- (for details, please refer to the GINSim manual http://ginsim.org/ginsim-doc/current/format-truthtable.html )
- The first line contains a space/tab separated list of the names of the variables.
- The second to last lines consist of two columns separated by space/tab; each line contains a source state followed by its corresponding target state. (thus, the maximum value for each gene is restricted to 9)