TY - JOUR
T1 - Bio-Logic Builder
T2 - A Non-Technical Tool for Building Dynamical, Qualitative Models
AU - Helikar, Tomáš
AU - Kowal, Bryan
AU - Madrahimov, Alex
AU - Shrestha, Manish
AU - Pedersen, Jay
AU - Limbu, Kahani
AU - Thapa, Ishwor
AU - Rowley, Thaine
AU - Satalkar, Rahul
AU - Kochi, Naomi
AU - Konvalina, John
AU - Rogers, Jim A.
PY - 2012/10/17
Y1 - 2012/10/17
N2 - 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.
AB - 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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U2 - 10.1371/journal.pone.0046417
DO - 10.1371/journal.pone.0046417
M3 - Article
C2 - 23082121
AN - SCOPUS:84867637547
SN - 1932-6203
VL - 7
JO - PloS one
JF - PloS one
IS - 10
M1 - e46417
ER -