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.
Highlights
Logical models are highly abstract dynamical models, which have been proposed to study biological regulatory systems in the late 60s (Kauffman, 1969; Thomas, 1973)
These effects are further formalized as logical rules, BioLQM Toolkit specifying the target activity level of each component according to the current levels of its regulators
The increasing use of logical models of biological regulatory networks led to the development of multiple complementary software tools for their analysis
Summary
Logical models are highly abstract dynamical models, which have been proposed to study biological regulatory systems in the late 60s (Kauffman, 1969; Thomas, 1973). BioLQM is notably embed in the popular GINsim software (Naldi et al, 2018a), which provides a graphical interface to most of its features It is used as backend for model definition and computation of successor states in Epilog (Varela et al, 2013), as well as in the CoLoMoTo notebook for model conversion and some dynamical analysis features (Naldi et al, 2018b). Preliminary versions of this toolkit were mentioned as the “LogicalModel” library Chaouiya et al (2013) and Naldi et al (2015).
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