A multilevel to Boolean gene regulatory network converter
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README.md
example.tt
multi2boolean.pl

README.md

multi2boolean

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)