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 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.
Department of Mathematics, University of Nebraska at Omaha, Omaha, Nebraska, USA. thelikar@unomaha.edu
Tomáš
T
Helikar
Bryan
B
Kowal
Alex
A
Madrahimov
Manish
M
Shrestha
Jay
J
Pedersen
Kahani
K
Limbu
Ishwor
I
Thapa
Thaine
T
Rowley
Rahul
R
Satalkar
Naomi
N
Kochi
John
J
Konvalina
Jim A
JA
Rogers
D000465:Algorithms; D003198:Computer Simulation; D020407:Internet; D008128:Logic; D008954:Models, Biological; D015398:Signal Transduction; D014584:User-Computer Interface; D020744:rac GTP-Binding Proteins / Q000378:metabolism
D020744:rac GTP-Binding Proteins