title: MOSBIE: a tool for comparison and analysis of rule-based biochemical models.
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.
authors.forename: John E
authors.initials: JE
authors.lastname: Wenskovitch
authors.forename: Leonard A
authors.initials: LA
authors.lastname: Harris
authors.forename: Jose-Juan
authors.initials: JJ
authors.lastname: Tapia
authors.forename: James R
authors.initials: JR
authors.lastname: Faeder
authors.affiliation: Electronic Visualization Lab, Department of Computer Science, University of Illinois at Chicago, 60607 Chicago, USA. g.elisabeta.marai@gmail.com.
authors.forename: G Elisabeta
authors.initials: GE
authors.lastname: Marai
mesh_terms: D008954:Models, Biological; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000379:methods*