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Research

RuleBender: Visual Debuggers for Diagram-Based Biological Models

Themes People Videos Talks Sponsors Publications Bibliography

Status: Active

This project develops interaction and visualization paradigms to allow the collaborative development of diagram-based computational biology models. Such models draw on the expertise of biologists, who are not necessarily experts in mathematical modeling, while providing the deeper insights into the simulation process that are needed for such tasks as model and simulation debugging, and overall understanding of molecular systems.

Themes

Biological Systems Modeling and Visualization

People

James Faeder
Liz Marai
Adam Smith
Yao Sun
John Wenskovitch
Wen Xu

Sponsors

Pitt Clinical and Translational Sciences Institute (Fellows Program) 5UL1RR024153-05 (RuleBender)

NSF CAREER IIS-0952720 *old* (Tracking, Computational Modeling and Interdisciplinary Edu)

NSF CAREER IIS-1541277 *new* (Tracking, Computational Modeling and Interdisciplinary Edu)

Videos

Cellucidate RuleStudio Eclipse Plugin

 



Talks

 



 

Publications

2015
J. Aerts, G.E. Marai, K. Nieselt, C. Nielsen, M. Streit, D. Weiskopf, "Highlights from the 5th Symposium on Biological Data Visualization: Part 1", BMC Bioinformatics, Vol. 16(0), pp. 1--2, 2015. (bibtex: Aerts-2015-HFT).
J. Aerts2, G.E. Marai, K. Nieselt, C. Nielsen, M. Streit, D. Weiskopf, "Highlights from the 5th Symposium on Biological Data Visualization: Part 2", BMC Proceedings, Vol. 9(0), pp. 1--2, 2015. (bibtex: Aerts2-2015-HFT).
J. Aurisano, K. Reda, A. Johnson, G.E. Marai, J. Leigh, "BactoGeNIE: A Large-Scale Comparative Genome Visualization for Big Displays", BMC Bioinformatics, Vol. 16(0), pp. 1--13, 2015. (pdf) (bibtex: Aurisano-2015-BAL).

2014
G.E. Marai, S. O’Donoghue, C. Bartlett and J. Aerts (editors), "BMC Bioinformatics Biological Data Visualization Series", BioMed Central, Vol. 0(0), pp. 1--100, 2014. (bibtex: Marai-2014-BBB).
J. Wenskovitch, L.A. Harris, J.J. Tapia, J.R. Faeder, G.E. Marai, "MOSBIE: A Tool for Comparison and Analysis of Rule-Based Biochemical Models", BMC Bioinformatics Journal 15:316, Vol. 15(0), pp. 1--22, 2014. (pdf) (bibtex: Wenskovitch-2014-MAT).

2012
A. M. Smith, "INTEGRATED MODELING, SIMULATION, AND VISUALIZATION FOR RULE-BASED INTRACELLULAR BIOCHEMISTRY", Master's Thesis, Vol. 0(4), pp. 0--0, Apr 2012. (pdf) (bibtex: Smith-2012-IMS).
A.M. Smith, W. Xu, Y. Sun, J.R. Faeder, G.E. Marai, "RuleBender: Integrated Modeling, Simulation and Visualization for Rule-Based Intracellular Biochemistry", BMC Journal of Bioinformatics, Vol. 13(6), pp. 1--16, Jun 2012. (pdf) (bibtex: Smith-2012-RIM).

2011
IEEE BioVis'11 Best Paper Award
A.M. Smith, W. Xu, Y. Sun, J.R. Faeder, G.E. Marai, "RuleBender: Integrated Visualization for Biochemical Rule-Based Modeling", IEEE Visualization 2011, IEEE BioVIs: Symposium on Biological Data Visualization, pp. 1--8, Oct 2011. (pdf) (bibtex: Smith-2011-RIV).

A. Smith, W. Xu, J.R. Faeder, G.E. Marai, "Scalable Global Views for Biological Rule-Based Modeling", IEEE Visualization 2011, Information Visualization, Poster Abstracts with System Demonstration, pp. 1--2, Oct 2011. (pdf) (bibtex: Smith-2011-SGV).
W. Xu, A. Smith, J.R. Faeder, G.E. Marai, "RuleBender: A Visual Interface for Rule-Based Modeling", Bioinformatics Journal, Vol. 27(4), pp. 1721--2, Apr 2011. (pdf) (bibtex: Xu-2011-RAV).

2010

A.M. Smith, W. Xu, Y. Sun, J.R. Faeder, G.E. Marai, "Visual Tools for Modeling and Simulation of Cell Signaling Networks ", Carnegie Mellon University Bioimaging Informatics Symposium, pp. 1--1, Sep 2010. (pdf) (bibtex: A.M. Smith-2010-VTF).
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