Rule-based modeling allows for the construction and simulation of models representing chemical interactions within and between cells. The iterative development of these models presents several challenges, including keeping track of the features encoded in each model and understanding the development history of the family of models.

In this work, we present the development and features of a journaling system to meet these challenges. A small multiples view displays the contact map rendering of each model in the development family. Users can interactively compare the similarities and differences between pairs of models, or search for models which contain an individual structure. A history tree view shows the development of the model family with respect to time.

More information about the project, as well as a download link, can be found at the official website.

Related Publications:

• John Wenskovitch, Leonard A. Harris, Jose-Juan Tapia, James R. Faeder, and G. Elisabeta Marai. “MOSBIE: A Tool for Comparison and Analysis of Rule-Based Biochemical Models,” BMC Bioinformatics, 15(1) (2014), pp. 316–331. DOI: 10.1186/1471-2105-15-316. Journal Impact Factor: 2.213.
• John Wenskovitch, Leonard Harris, James Faeder, and G. Elisabeta Marai. “A Journaling System for Rule-Based Biochemical Models,” in IEEE BioVis Poster Abstracts with System Demonstration. Atlanta, GA, 2013.