A Model Browser for Biosimulation

The complexities of biological simulation present difficulties with modeling and experimenting. Simulators process models represented as code, whereas biologists think about abstract models. Our ModelBrowser addresses this difficulty through interactive visualization. Variables and equations appear as a directed graph of nodes and edges, and the user can search and browse this graph by performing queries on metadata associated with the variables and the connectivity of the edges. The browser also supports a hierarchical categorization of the variables, such as by an ontology. We believe that the ModelBrowser will help biologists reason about code in the context of the abstract model, so that they can understand and modify others' code and debug their own.

[1]  José L. V. Mejino,et al.  Evolution of a Foundational Model of Physiology: Symbolic Representation for Functional Bioinformatics , 2004, MedInfo.

[2]  Daniel L. Rubin,et al.  Ontology-Based Representation of Simulation Models of Physiology , 2006, AMIA.

[3]  John H. Gennari,et al.  Pacific Symposium on Biocomputing 12:16-27(2007) CHALKBOARD: ONTOLOGY-BASED PATHWAY MODELING AND QUALITATIVE INFERENCE OF DISEASE MECHANISMS , 2022 .

[4]  Chris R. Johnson.  Top Scientific Visualization Research Problems , 2004, IEEE Computer Graphics and Applications.

[5]  Ben Shneiderman,et al.  Visual information seeking: tight coupling of dynamic query filters with starfield displays , 1994, CHI Conference Companion.

[6]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[7]  Jeffrey Heer,et al.  prefuse: a toolkit for interactive information visualization , 2005, CHI.

[8]  Ben Shneiderman,et al.  Visual Information Seeking: Tight Coupling of Dynamic Query Filters with Starfield Displays , 1994 .

[9]  Danny Holten,et al.  Hierarchical Edge Bundles: Visualization of Adjacency Relations in Hierarchical Data , 2006, IEEE Transactions on Visualization and Computer Graphics.

[10]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[11]  Peter J. Hunter,et al.  Modeling Human Physiology: The IUPS/EMBS Physiome Project , 2006, Proceedings of the IEEE.

[12]  Neil A. Ernst,et al.  Jambalaya: an interactive environment for exploring ontologies , 2002, IUI '02.

[13]  Ben Shneiderman,et al.  Readings in information visualization - using vision to think , 1999 .