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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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Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3474764/
https://www.ncbi.nlm.nih.gov/pubmed/23082121
http://dx.doi.org/10.1371/journal.pone.0046417
Descripción
Sumario: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.