Bio-logic builder: a non-technical tool for building dynamical, qualitative models.
Bio-logic builder: a non-technical tool for building dynamical, qualitative models.
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DOI：
10.1371/journal.pone.0046417
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Rogers JA
中科院分区：
文献类型：
--
作者：
Helikar T;Kowal B;Madrahimov A;Shrestha M;Pedersen J;Limbu K;Thapa I;Rowley T;Satalkar R;Kochi N;Konvalina J;Rogers JA
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.
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