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Open Access Software

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

Alida Palmisano12*, Stefan Hoops3, Layne T Watson14, Thomas C Jones Jr1, John J Tyson2 and Clifford A Shaffer1

Author Affiliations

1 Department of Computer Science, Virginia Polytechnic and State University, 2202 Kraft Drive, Blacksburg, VA 24060, USA

2 Department of Biological Sciences, Virginia Polytechnic and State University, 1405 Perry Street, Blacksburg, VA 24061, USA

3 Virginia Bioinformatics Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA

4 Department of Mathematics, Virginia Polytechnic and State University, 225 Stanger Street, Blacksburg, VA 24061, USA

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BMC Systems Biology 2014, 8:42  doi:10.1186/1752-0509-8-42

Published: 4 April 2014

Abstract

Background

Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of today’s biochemical model editors. Our model editor MSMB — Multistate Model Builder — supports multistate models created using different modeling styles.

Results

MSMB provides two separate advances on existing network model editors. (1) A simple but powerful syntax is used to describe multistate species. This reduces the number of reactions needed to represent certain molecular systems, thereby reducing the complexity of model creation. (2) Extensive feedback is given during all stages of the model creation process on the existing state of the model. Users may activate error notifications of varying stringency on the fly, and use these messages as a guide toward a consistent, syntactically correct model. MSMB default values and behavior during model manipulation (e.g., when renaming or deleting an element) can be adapted to suit the modeler, thus supporting creativity rather than interfering with it. MSMB’s internal model representation allows saving a model with errors and inconsistencies (e.g., an undefined function argument; a syntactically malformed reaction). A consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB’s multistate syntax through models of the cell cycle and mRNA transcription.

Conclusions

Using multistate reactions reduces the number of reactions need to encode many biochemical network models. This reduces the cognitive load for a given model, thereby making it easier for modelers to build more complex models. The many interactive editing support features provided by MSMB make it easier for modelers to create syntactically valid models, thus speeding model creation. Complete information and the installation package can be found at http://www.copasi.org/SoftwareProjects webcite. MSMB is based on Java and the COPASI API.

Keywords:
Systems biology; Biological networks; Mathematical modeling; Chemical reaction systems; COPASI; SBML; Software; Model editor; Multistate