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BMC Syst Biol. 2015 Dec 24;9:95. doi: 10.1186/s12918-015-0237-0.

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations.

Author information

1
Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. alida.palmisano@gmail.com.
2
Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA. alida.palmisano@gmail.com.
3
Virginia Bioinformatics Institute, 1015 Life Science Circle, Blacksburg, 24061, VA, USA. shoops@vbi.vt.edu.
4
Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. ltw@vt.edu.
5
Department of Mathematics, Virginia Tech, 225 Stanger Street, Blacksburg, 24061, VA, USA. ltw@vt.edu.
6
Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. tjones21@vt.edu.
7
Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA. tyson@vt.edu.
8
Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. shaffer@cs.vt.edu.

Abstract

BACKGROUND:

Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different parameterizations of the model to account for the results of related experiments, for example, to define the phenotypes for a variety of mutations (gene knockout, over expression, etc.) of a specific biochemical network. This scenario is not well supported by existing model editors, forcing the user to manually generate, store, and maintain many variations of the same model.

RESULTS:

We developed an extension to our modeling editor called the JigCell Run Manager (JC-RM). JC-RM allows the modeler to define a hierarchy of parameter values, simulations, and plot settings, and to save them together with the initial model. JC-RM supports generation of simulation plots, as well as export to COPASI and SBML (L3V1) for further analysis.

CONCLUSIONS:

Developing a model with its initial list of parameter values is just the first step in modeling a biological system. Models are often parameterized in many different ways to account for mutations of the organism and/or for sets of related experiments performed on the organism. JC-RM offers two critical features: it supports the everyday management of a large model, complete with its parameterizations, and it facilitates sharing this information before and after publication. JC-RM allows the modeler to define a hierarchy of parameter values, simulation, and plot settings, and to maintain a relationship between this hierarchy and the initial model. JC-RM is implemented in Java and uses the COPASI API. JC-RM runs on all major operating systems, with minimal system requirements. Installers, source code, user manual, and examples can be found at the COPASI website ( http://www.copasi.org/Projects ).

PMID:
26704692
PMCID:
PMC4690432
DOI:
10.1186/s12918-015-0237-0
[Indexed for MEDLINE]
Free PMC Article

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