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

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, ex...

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Detalles Bibliográficos
Autores principales: Gündel, Michaela, Hoyt, Charles Tapley, Hofmann-Apitius, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022644/
https://www.ncbi.nlm.nih.gov/pubmed/29949955
http://dx.doi.org/10.1093/bioinformatics/bty107
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author Gündel, Michaela
Hoyt, Charles Tapley
Hofmann-Apitius, Martin
author_facet Gündel, Michaela
Hoyt, Charles Tapley
Hofmann-Apitius, Martin
author_sort Gündel, Michaela
collection PubMed
description 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.
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spelling pubmed-60226442018-07-10 BEL2ABM: agent-based simulation of static models in Biological Expression Language Gündel, Michaela Hoyt, Charles Tapley Hofmann-Apitius, Martin Bioinformatics Applications Notes 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. Oxford University Press 2018-07-01 2018-02-23 /pmc/articles/PMC6022644/ /pubmed/29949955 http://dx.doi.org/10.1093/bioinformatics/bty107 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Gündel, Michaela
Hoyt, Charles Tapley
Hofmann-Apitius, Martin
BEL2ABM: agent-based simulation of static models in Biological Expression Language
title BEL2ABM: agent-based simulation of static models in Biological Expression Language
title_full BEL2ABM: agent-based simulation of static models in Biological Expression Language
title_fullStr BEL2ABM: agent-based simulation of static models in Biological Expression Language
title_full_unstemmed BEL2ABM: agent-based simulation of static models in Biological Expression Language
title_short BEL2ABM: agent-based simulation of static models in Biological Expression Language
title_sort bel2abm: agent-based simulation of static models in biological expression language
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022644/
https://www.ncbi.nlm.nih.gov/pubmed/29949955
http://dx.doi.org/10.1093/bioinformatics/bty107
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