ModRev is a command line tool to revise Boolean logical models of biological regulatory networks.

This tool was developed for UNIX and MacOSX systems.

ModRev is able to repair inconsistent Boolean models under the following:

• Set of stable state observations
• Set of time-series observations
  • With synchronous update scheme
  • With asynchronous update scheme

Releases

• ModRev v1.3.2
• ModRev v1.3.1
• ModRev v1.2.3 (only supports either stable state or time-series observations but not both simultaneously)
• ModRev v1.1.0 (only supports stable state observations)

Additional material

• Examples of inconsistent networks: inputNetworks
• Examples of time-series observations: observations

Validation

Check here for more information about experimental validation.

Publications

• F. Gouveia, I. Lynce, P.T. Monteiro (2020)
  ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks
  in A. Abate, T. Petrov, V. Wolf (editors)
  Computational Methods in Systems Biology (CMSB 2020), LNCS 12314, 339-348, Springer
  doi:10.1007/978-3-030-60327-4_18

• F. Gouveia, I. Lynce, P.T. Monteiro (2020)
  Revision of Boolean models of regulatory networks using stable state observations
  Journal of Computational Biology, 27(2): 144-155
  doi:10.1089/cmb.2019.0289

• F. Gouveia, I. Lynce, P.T. Monteiro (2019)
  Model revision of Boolean regulatory networks at stable state
  in Z. Cai et al. (editors)
  Proc. of the 15th International Symposium on Bioinformatics Research and Applications (ISBRA’19), LNCS 11490, 1-13
  doi:10.1007/978-3-030-20242-2_9

Thesis

• F. Gouveia (2021)
  Model Revision of Boolean Logical Models of Biological Regulatory Networks
  PhD Thesis in Computer Science and Engineering, Instituto Superior Técnico, Universidade de Lisboa
  Thesis (Bibtex)

Authors

• Filipe Gouveia
• Inês Lynce
• Pedro Monteiro

Contact

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