Biocomputation Group
at the University of Pennsylvania
   
 


 

Question or Comment
Contact: Valentina Sokolskaya
Last updated: January 10, 05

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.

Biochemical pathways

You can model the dynamics of complicated pathways including molecular reactions, cell diffusion and growth, inhibition mechanisms, and genetic regulation.

Simulation

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 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

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

Development

BSP was developed by

Calin Belta, Mark Goulian, Franjo Ivancic, 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).

BSP is available for download with the CHARON simulation tools from here.

For more information, contact

Harvey Rubin
rubinh@mail.med.upenn.edu

Vijay Kumar
Kumar@cis.upenn.edu

Arch Owen
Aowen@bbn.com