Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules

Ryan Suderman; G Matthew Fricke; William S Hlavacek

doi:10.1007/978-1-4939-9102-0_2

Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules

Methods Mol Biol. 2019:1945:33-42. doi: 10.1007/978-1-4939-9102-0_2.

Authors

Ryan Suderman^{1

2}, G Matthew Fricke³, William S Hlavacek⁴

Affiliations

¹ Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.
² Immunetrics, Inc., Pittsburgh, PA, USA.
³ Department of Computer Science, University of New Mexico, Albuquerque, NM, USA.
⁴ Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. wish@lanl.gov.

PMID: 30945241
DOI: 10.1007/978-1-4939-9102-0_2

Abstract

RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems. BNGL provides an intuitive plain text, or string, representation of such systems, which is based on a graphical formalism. Reactions are defined in terms of graph-rewriting rules that specify the necessary intrinsic properties of the reactants, a transformation, and a rate law. Rules also contain contextual constraints that restrict application of the rule. In some cases, the specification of contextual constraints can be verbose, making a rule difficult to read. RuleBuilder is designed to ease the task of reading and writing individual reaction rules or other BNGL patterns required for model formulation. The software assists in the reading of existing models by converting BNGL strings of interest into a graph-based representation composed of nodes and edges. RuleBuilder also enables the user to construct de novo a visual representation of BNGL strings using drawing tools available in its interface. As objects are added to the drawing canvas, the corresponding BNGL string is generated on the fly, and objects are similarly drawn on the fly as BNGL strings are entered into the application. RuleBuilder thus facilitates construction and interpretation of rule-based models.

Keywords: Chemical kinetics; Drawing tool; Dynamical systems; Graph rewriting; Mathematical modeling; Rule-based modeling; Software; Systems biology; Visualization.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Computer Simulation*
Models, Biological
Models, Theoretical*
Signal Transduction / genetics
Software*

Grants and funding

R01 GM111510/GM/NIGMS NIH HHS/United States