BEL2ABM: agent-based simulation of static models in Biological Expression Language

Authored by Michaela Guendel, Charles Tapley Hoyt, Martin Hofmann-Apitius

Date Published: 2018

DOI: 10.1093/bioinformatics/bty107

Sponsors: No sponsors listed

Platforms: NetLogo

Model Documentation: Other Narrative

Model Code URLs: https://github.com/pybel/bel2abm

Abstract

While cause-and-effect knowledge assembly models encoded in Biological Expression Language are able to support generation of mechanistic hypotheses, they are static and limited in their ability to encode temporality. Here, we present BEL2ABM, a software for producing continuous, dynamic, executable agent-based models from BEL templates. Availability and implementation: The tool has been developed in Java and NetLogo. Code, data and documentation are available under the Apache 2.0 License at https://github.com/pybel/bel2abm. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

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