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BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks
Here we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations as building blocks for the development of integrated modeling software, or for the assembly o...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6254088/ https://www.ncbi.nlm.nih.gov/pubmed/30510517 http://dx.doi.org/10.3389/fphys.2018.01605 |
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author | Naldi, Aurélien |
author_facet | Naldi, Aurélien |
author_sort | Naldi, Aurélien |
collection | PubMed |
description | Here we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations as building blocks for the development of integrated modeling software, or for the assembly of heterogeneous analysis workflows involving several complementary tools. Based on the definition of multi-valued logical models, bioLQM implements import and export facilities, notably for the recent SBML qual exchange format, as well as for formats used by several popular tools, facilitating the design of workflows combining these tools. Model modifications enable the definition of various perturbations, as well as model reduction, easing the analysis of large models. Another modification enables the study of multi-valued models with tools limited to the Boolean case. Finally, bioLQM provides a framework for the development of novel analysis tools. The current version implements various updating modes for model simulation (notably synchronous, asynchronous, and random asynchronous), as well as some static analysis features for the identification of attractors. The bioLQM software can be integrated into analysis workflows through command line and scripting interfaces. As a Java library, it further provides core data structures to the GINsim and EpiLog interactive tools, which supply graphical interfaces and additional analysis methods for cellular and multi-cellular qualitative models. |
format | Online Article Text |
id | pubmed-6254088 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-62540882018-12-03 BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks Naldi, Aurélien Front Physiol Physiology Here we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations as building blocks for the development of integrated modeling software, or for the assembly of heterogeneous analysis workflows involving several complementary tools. Based on the definition of multi-valued logical models, bioLQM implements import and export facilities, notably for the recent SBML qual exchange format, as well as for formats used by several popular tools, facilitating the design of workflows combining these tools. Model modifications enable the definition of various perturbations, as well as model reduction, easing the analysis of large models. Another modification enables the study of multi-valued models with tools limited to the Boolean case. Finally, bioLQM provides a framework for the development of novel analysis tools. The current version implements various updating modes for model simulation (notably synchronous, asynchronous, and random asynchronous), as well as some static analysis features for the identification of attractors. The bioLQM software can be integrated into analysis workflows through command line and scripting interfaces. As a Java library, it further provides core data structures to the GINsim and EpiLog interactive tools, which supply graphical interfaces and additional analysis methods for cellular and multi-cellular qualitative models. Frontiers Media S.A. 2018-11-19 /pmc/articles/PMC6254088/ /pubmed/30510517 http://dx.doi.org/10.3389/fphys.2018.01605 Text en Copyright © 2018 Naldi. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Physiology Naldi, Aurélien BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks |
title | BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks |
title_full | BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks |
title_fullStr | BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks |
title_full_unstemmed | BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks |
title_short | BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks |
title_sort | biolqm: a java toolkit for the manipulation and conversion of logical qualitative models of biological networks |
topic | Physiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6254088/ https://www.ncbi.nlm.nih.gov/pubmed/30510517 http://dx.doi.org/10.3389/fphys.2018.01605 |
work_keys_str_mv | AT naldiaurelien biolqmajavatoolkitforthemanipulationandconversionoflogicalqualitativemodelsofbiologicalnetworks |