Bio-Logic Builder

A Non-Technical Tool for Building Dynamical, Qualitative Models

Tomas Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim A Rogers

Research output: Contribution to journalArticle

9 Citations (Scopus)

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 "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.

Original languageEnglish (US)
Article numbere46417
JournalPloS one
Volume7
Issue number10
DOIs
StatePublished - Oct 17 2012

Fingerprint

Biological Phenomena
Laboratory Personnel
Saccharomycetales
Mathematics
Signal transduction
Human Influenza
Biomedical Research
Signal Transduction
Cell Cycle
Research laboratories
user interface
computer science
Yeast
Computer science
User interfaces
biomedical research
influenza
Cells
signal transduction
cell cycle

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Bio-Logic Builder : A Non-Technical Tool for Building Dynamical, Qualitative Models. / Helikar, Tomas; Kowal, Bryan; Madrahimov, Alex; Shrestha, Manish; Pedersen, Jay; Limbu, Kahani; Thapa, Ishwor; Rowley, Thaine; Satalkar, Rahul; Kochi, Naomi; Konvalina, John; Rogers, Jim A.

In: PloS one, Vol. 7, No. 10, e46417, 17.10.2012.

Research output: Contribution to journalArticle

Helikar, T, Kowal, B, Madrahimov, A, Shrestha, M, Pedersen, J, Limbu, K, Thapa, I, Rowley, T, Satalkar, R, Kochi, N, Konvalina, J & Rogers, JA 2012, 'Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models', PloS one, vol. 7, no. 10, e46417. https://doi.org/10.1371/journal.pone.0046417
Helikar, Tomas ; Kowal, Bryan ; Madrahimov, Alex ; Shrestha, Manish ; Pedersen, Jay ; Limbu, Kahani ; Thapa, Ishwor ; Rowley, Thaine ; Satalkar, Rahul ; Kochi, Naomi ; Konvalina, John ; Rogers, Jim A. / Bio-Logic Builder : A Non-Technical Tool for Building Dynamical, Qualitative Models. In: PloS one. 2012 ; Vol. 7, No. 10.
@article{fe3dc723cb984328862347aed886a66e,
title = "Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models",
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 {"}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.",
author = "Tomas Helikar and Bryan Kowal and Alex Madrahimov and Manish Shrestha and Jay Pedersen and Kahani Limbu and Ishwor Thapa and Thaine Rowley and Rahul Satalkar and Naomi Kochi and John Konvalina and Rogers, {Jim A}",
year = "2012",
month = "10",
day = "17",
doi = "10.1371/journal.pone.0046417",
language = "English (US)",
volume = "7",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

TY - JOUR

T1 - Bio-Logic Builder

T2 - A Non-Technical Tool for Building Dynamical, Qualitative Models

AU - Helikar, Tomas

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.

UR - http://www.scopus.com/inward/record.url?scp=84867637547&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84867637547&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0046417

DO - 10.1371/journal.pone.0046417

M3 - Article

VL - 7

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e46417

ER -