Work

GetBonNie for building, analyzing and sharing rule-based models

Year: 2009

Type: article

Abstract: SUMMARY: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results. AVAILABILITY: GetBonNie is free at (http://getbonnie.org).

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btp173

Authors: Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek

Institutions: Translational Genomics Research Institute, Los Alamos National Laboratory, University of New Mexico, University of Pittsburgh

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: U.S. Department of Energy, National Institutes of Health, National Cancer Institute, National Institute of General Medical Sciences

Awards: G286898171, G5657628048, G5713387433, Targets to Therapeutics in Pancreatic Cancer, COMPUTATIONAL TOOLS FOR RULE-BASED MODELING OF BIOCHEMICAL SYSTEMS