Bio Sketch Pad
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.
You can model the dynamics of complicated pathways including molecular
reactions, cell diffusion and growth, inhibition mechanisms, and genetic
BSP generates formal CHARON models enabling analysis and simulation.
The user interface
BSP is easy-to-navigate with pull-down menus for creating species, templates
for reactions, and wizards for creating pathways.
This model of V. fischeri, developed in collaboration with Paul Dunlap
(Univ. of Michigan), analyzes an example of bioluminescence in bacteria.
The BSP advantage
BSP is a collaboration between academia and industry
- 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.
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
BSP was developed by
Calin Belta, Mark Goulian, Franjo Ivancic, Vijay Kumar, Harvey Rubin,
Jonathan Schug, and Oleg Sokolsky at the University of Pennslvania
Sharon Gowen, Arch Owen, Matt Ruben, Jonathan Webb, and Lois Welber at BBN
with support from Defense Advanced Research Projects Agency (DARPA).
BSP is available for download with the CHARON simulation tools from
For more information, contact