“RuleBender” Recognized with Test of Time Award

July 26th, 2021

Categories: Applications, User Groups, Visualization, Visual Analytics, Visual Informatics, Data Science


G. Elisabeta Marai and collaborators are recognized with the 10-years Test of Time award at ISMB 2021, the flagship conference for computational biology, for the most impactful paper on biovisualization, awarded by the BioVis ISMB COSI (a COSI is a main track at the ISMB conference). The award was made to: Smith AM, Xu W, Sun Y, Faeder JR, Marai GE. “RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.” BMC Bioinformatics. 2012 Dec;13(8):1-6. This research was originally presented at the 2011 Conference, and is listed a later year due to the journal publication model. RuleBender is a system for the rule-based visualization, modeling and simulation of intracellular biochemistry.

Beyond the impressive citation record, which shows that this work informed both bioinformatics research and data visualization research, RuleBender is alive and well. It has been remarkably stable over the past ten years, it is still downloaded and used, averaging about 1000 downloads per year in the past five years alone. It has been adopted at over 40 institutions as a research and educational tool. It has been used by at least hundreds of computational biologists to do real and high impact research all over the world, from Ghana to Canada.

Co-authors Adam, Wen and Yao were Marai’s Masters students in 2011 and are now senior software engineers at Argo AI, Microsoft, and Amazon. Jim was a collaborator in Systems Biology at Pitt/CMU.