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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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Autor principal: Naldi, Aurélien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
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.
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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