A Tool for Comparison and Analysis of Rule-Based Biochemical Models

John R. Wenskovitch, Leonard A. Harris, Jose-Juan Tapia,
James R. Faeder, G. Elisabeta Marai


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 network models, either by a single research group or from multiple sources, presents significant challenges that range from identifying functional structural differences to keeping track of the model history. We present the development and features of an interactive model exploration system, MOSBIE, which tracks the features and development history of a family of models and provides utilities for identifying similarities and differences between models. Models within a collection can be clustered using a custom similarity metric. We also provide a visual interface for exploring collections of models, allowing a researcher to interactively compare the similarities and differences between pairs of models, search for models which contain a given structural motif, and explore the parameters and simulations of models. We evaluate the usefulness of this system with a case study in the cell signaling domain. We present the feedback provided by domain experts, and discuss the benefits of this approach.

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


Here you can get the MOSBIE executables; the MOSBIE code is built on top of the latest release of RuleBender:

We no longer support the following executables, which you may use at your own risk: