Bio-logic builder: a non-technical tool for building dynamical, qualitative models

Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help...

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Published in:	PloS one Vol. 7; no. 10; p. e46417
Main Authors:	Helikar, Tomáš, Kowal, Bryan, Madrahimov, Alex, Shrestha, Manish, Pedersen, Jay, Limbu, Kahani, Thapa, Ishwor, Rowley, Thaine, Satalkar, Rahul, Kochi, Naomi, Konvalina, John, Rogers, Jim A
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 17-10-2012 Public Library of Science (PLoS)
Subjects:	Algorithms Analysis Bioinformatics Biological activity Biological computing Biological models (mathematics) Biology Boolean algebra Cell cycle Computation Computer applications Computer Science Computer Simulation Influenza A Information science Internet Kinases Laboratories Large-scale models Logic Mathematical analysis Mathematical models Mathematics Models, Biological Phosphorylation Proteins Qualitative research rac GTP-Binding Proteins - metabolism Regulation Regulatory mechanisms (biology) Representations Science Scientists Signal Transduction Software Systems biology Transduction Trends User-Computer Interface Yeast United States > US Nebraska
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Summary:	Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized "bio-logic" modules have been defined to provide users with the building blocks for many biological processes. To build/modify computational models, experimentalists provide purely qualitative information about a particular regulatory mechanisms as is generally found in the laboratory. The Bio-Logic Builder subsequently converts the provided information into a mathematical representation described with Boolean expressions/rules. We used this tool to build a number of dynamical models, including a 130-protein large-scale model of signal transduction with over 800 interactions, influenza A replication cycle with 127 species and 200+ interactions, and mammalian and budding yeast cell cycles. We also show that any and all qualitative regulatory mechanisms can be built using this tool.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Competing Interests: The authors have declared that no competing interests exist. Conceived and designed the experiments: TH JAR. Performed the experiments: TH BK KL IT MS NK RS TR AM. Analyzed the data: TH JAR JP JK AM. Contributed reagents/materials/analysis tools: JP JK. Wrote the paper: TH JAR.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0046417