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B io S ketch P ad

BSP. B io S ketch P ad. BSP. Biochemical pathways. Development.

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B io S ketch P ad

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  1. BSP Bio Sketch Pad BSP Biochemical pathways Development BSP is an interactive tool for modeling and designing biomolecular and cellular networks with a simple, easy-to-use, graphical front end, leveraging powerful tools from control theory, hybrid systems, and software engineering. BSP was developed by Calin Belta, Mark Goulian, Franjo Ivančić, Vijay Kumar, Harvey Rubin, Jonathan Schug, and Oleg Sokolsky at the University of Pennslvania and Sharon Gowen, Arch Owen, Matt Ruben, Jonathan Webb, and Lois Welber at BBN Technologies with support from Defense Advanced Research Projects Agency (DARPA). You can model the dynamics of complicated pathways including molecular reactions, cell diffusion and growth, inhibition mechanisms, and genetic regulation. More information about BSP and the BioComp program is available at http://www.cis.upenn.edu/biocomp • BSP was developed by funding from the BioComp program, DARPA IPTO, and is available for download with the CHARON simulation tools from • http://bio.bbn.com/biospice/biosketchpad/ • For more information, contact • Harvey Rubin rubinh@mail.med.upenn.edu • Vijay Kumar • Kumar@cis.upenn.edu • Arch Owen • Aowen@bbn.com Simulation BSP generates formal CHARON models enabling analysis and simulation.

  2. BSP BSP BSP The user interface • The BSP advantage • BSP was designed with biologists for biologists; • BSP allows experimentalists to easily generate working models of networks; • BSP uses the theory of hybrid systems to model discrete and continuous phenomena that are inherent in biological systems; • BSP brings modern tools of hierarchy, modularity and concurrency from software engineering; and • BSP leverages the development of CHARON language and tool set. BSP is a collaboration between academia and industry Architecture diagram CHARON, a high-level programming language, is used to model the hybrid biological system. Biologists can use BSP as a front end to access the CHARON toolset which includes powerful modeling, analysis and simulation tools that have been developed at the University of Pennsylvania. CHARON was developed by the Hybrid Systems Group which includes Rajeev Alur, Vijay Kumar, Insup Lee, George Pappas and Oleg Sokolsky at the University of Pennsylvania with support from Defense Advanced Research Projects Agency (DARPA) and the National Science Foundation. BSP is easy-to-navigate with pull-down menus for creating species, templates for reactions, and wizards for creating pathways. Network Models The model of MTb dormancy describes one of the most important aspects of this infection, which is a major cause of death around the world This model of V. fischeri, developed in collaboration with Paul Dunlap (Univ. of Michigan), analyzes an example of bioluminescence in bacteria. More information about CHARON is available at http://www.cis.upenn.edu/charon

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