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MOSBIE: A tool for comparison and analysis of rule-based biochemical models

Wenskovitch, JE and Harris, LA and Tapia, JJ and Faeder, JR and Marai, GE (2014) MOSBIE: A tool for comparison and analysis of rule-based biochemical models. BMC Bioinformatics, 15 (1).

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Abstract

© 2014 Wenskovitch et al.; licensee BioMed Central Ltd. Background: Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presents significant challenges that range from identifying structural similarities and differences between models to understanding how these differences affect system dynamics.Results: We present the development and features of an interactive model exploration system, MOSBIE, which provides utilities for identifying similarities and differences between models within a family. Models are clustered using a custom similarity metric, and a visual interface is provided that allows a researcher to interactively compare the structures of pairs of models as well as view simulation results.Conclusions: We illustrate the usefulness of MOSBIE via two case studies in the cell signaling domain. We also present feedback provided by domain experts and discuss the benefits, as well as the limitations, of the approach.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Wenskovitch, JE
Harris, LA
Tapia, JJ
Faeder, JRfaeder@pitt.eduFAEDER
Marai, GE
Date: 25 September 2014
Date Type: Publication
Journal or Publication Title: BMC Bioinformatics
Volume: 15
Number: 1
DOI or Unique Handle: 10.1186/1471-2105-15-316
Schools and Programs: School of Medicine > Computational and Systems Biology
Refereed: Yes
Date Deposited: 19 Sep 2016 16:53
Last Modified: 02 Feb 2019 14:55
URI: http://d-scholarship.pitt.edu/id/eprint/29488

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