BEL2ABM: agent-based simulation of static models in Biological Expression Language.
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ABSTRACT: Summary
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.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Gundel M
PROVIDER: S-EPMC6022644 | biostudies-literature | 2018 Jul
REPOSITORIES: biostudies-literature
Publications
BEL2ABM: agent-based simulation of static models in Biological Expression Language.
Gündel Michaela M Hoyt Charles Tapley CT Hofmann-Apitius Martin M
Bioinformatics (Oxford, England) 20180701 13
<h4>Summary</h4>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.<h4>Availability and implementation</h4>The tool has been developed in Java and NetLogo. Code, data and documentation are available under the Apac ...[more]
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