biolqm: a java toolkit for the manipulation and conversion of logical qualitative models of biological networks

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ID: 150078
2018
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Abstract
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.
Reference Key
naldi2018frontiersbiolqm: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Aurélien Naldi
Journal Journal of clinical and experimental dentistry
Year 2018
DOI
10.3389/fphys.2018.01605
URL
https://www.frontiersin.org/article/10.3389/fphys.2018.01605/full
Keywords
biological networks qualitative modeling

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