Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models

Authors

Tomáš Helikar, University of Nebraska-LincolnFollow
Bryan Kowal, University of Nebraska at OmahaFollow
Alex Madrahimov, University of Nebraska at Omaha
Manish Shrestha, University of Nebraska at Omaha
Jay Pedersen, University of Nebraska at Omaha
Kahani Limbu, University of Nebraska at Omaha
Ishwor Thapa, University of Nebraska at Omaha
Thaine Rowley, University of Nebraska at Omaha
Rahul Satalkar, University of Nebraska at Omaha
Naomi Kochi, University of Nebraska Medical Center
John Konvalina, University of Nebraska at Omaha
Jim A. Rogers, University of Nebraska at Omaha

Document Type

Article

Date of this Version

2012

Citation

Helikar T, Kowal B, Madrahimov A, Shrestha M, Pedersen J, et al. (2012) Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models. PLoS ONE 7(10): e46417. doi:10.1371/journal.pone.0046417

Comments

Copyright 2012 Helikar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Abstract

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 ‘‘biologic’’ 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.