MOSBIE: a tool for comparison and analysis of rule-based biochemical models.
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ABSTRACT: 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.
SUBMITTER: Wenskovitch JE
PROVIDER: S-EPMC4261755 | biostudies-literature | 2014 Sep
REPOSITORIES: biostudies-literature
Publications
MOSBIE: a tool for comparison and analysis of rule-based biochemical models.
Wenskovitch John E JE Harris Leonard A LA Tapia Jose-Juan JJ Faeder James R JR Marai G Elisabeta GE
BMC bioinformatics 20140925
<h4>Background</h4>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.< ...[more]
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