Paper Info
Title
Automated Inference Of Boolean Models From Molecular Interaction Maps Using Casq
Abstract
Motivation: Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap between static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner.Results: We developed CaSQ by defining conversion rules and logical formulas for inferred Boolean models according to the topology and the annotations of the starting molecular interaction maps. We used CaSQ to produce executable files of existing molecular maps that differ in size, complexity and the use of Systems Biology Graphical Notation (SBGN) standards. We also compared, where possible, the manually built logical models corresponding to a molecular map to the ones inferred by CaSQ. The tool is able to process large and complex maps built with CellDesigner (either following SBGN standards or not) and produce Boolean models in a standard output format, Systems Biology Marked Up Language-qualitative (SBML-qual), that can be further analyzed using popular modelling tools. References, annotations and layout of the CellDesigner molecular map are retained in the obtained model, facilitating interoperability and model reusability.
Year
DOI
Venue
2020
10.1093/bioinformatics/btaa484
BIOINFORMATICS
DocType
Volume
Issue
Journal
36
16
ISSN
Citations 
PageRank 
1367-4803
1
0.35
References 
Authors
0
6
Name
Order
Citations
PageRank
Sara Sadat Aghamiri110.35
Vidisha Singh210.35
Aurélien Naldi338326.11
Tomáš Helikar4747.13
Sylvain Soliman548435.02
Anna Niarakis632.44