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

BMC Bioinformatics

John E¹  Leonard A Harris⁴  Jose-Juan Tapia²  James R Faeder²  G Elisabeta Marai³ 

[1] Department of Computer Science, Allegheny College, 16335 Meadville, PA, USA

[2] Department of Computational and Systems Biology, University of Pittsburgh, 15260 Pittsburgh, USA

[3] Electronic Visualization Lab, Department of Computer Science, University of Illinois at Chicago, 60607 Chicago, USA

[4] Department of Cancer Biology, Vanderbilt University School of Medicine, 37232 Nashville, TN, USA

关键词: Cell signaling;    Rule-based modeling;    Visual computing;    Visualization;   

Others  :  1085818
DOI  :  10.1186/1471-2105-15-316

 received in 2014-04-20, accepted in 2014-09-16,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Wenskovitch et al.; licensee BioMed Central Ltd.

【 图 表 】

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