CSI Cell System Modeling and Simulation Platform

advances in computer software and hardware technology have made it possible for biologists to simulate cellular processes, such as biochemical reactions; however, up to this point, accessible tools to exploit the technology did not exist.

Technology Description

The Cell Systems Initiative (CSI) program at the UW has created a symbolic modeling language and integrated software platform to simulate cell systems.

The Cell System Modeling and Simulation Platform comprises three parts:

• "BALSA," the user interface
  BALSA allows users to represent cell systems both graphically and symbolically using a novel symbolic modeling language called BioGlyphics. BioGlyphics was created to provide a common and unambiguous language that could automatically generate simulations based on the Systems Biology Markup Language (SBML). BALSA's graphical interface also dynamically generates cartoon representations of models created using BioGlyphics.
  
  
• "Sigtran," the software simulation engine
  Sigtran is software specifically designed to enable biological researchers to carry out large-scale simulations and analyses of complex reactions and interactions, such as signal transduction pathways. Sigtran operates on documents created with SBML.
  
  
• "Scooby," the hardware simulation engine
  Scooby is unique in its ability to configure its hardware to the structure of the model being simulated. BALSA passes an SBML file containing the model description to Scooby. The Scooby compiler converts that model into a chip configuration. Scooby simulates biochemical reaction systems over 100 times faster than any Pentiums® processor, using only a single chip.
  
  

Business Opportunity

These platform technologies have many potential applications. Use of the tools in drug discovery efforts, for example, would likely result in tremendous savings of time and resources in bringing drugs to market.

The set of three technologies could be licensed and resold to end users such as molecular or systems biologists. The BALSA interface and Sigtran simulation software might be used by a consulting firm to perform design modeling for pharmaceutical clients. Clients could then purchase the hardware to run large-scale simulations as needed. The Scooby simulation hardware could be used for any application that requires very fast parallel processing of rate-based reactions.

Stage of Development

The system is currently integrated and functioning at a basic level. Refinements and improvements to the system are in development.

Intellectual Property Position

A patent has been filed for the Scooby hardware technology. BALSA and Sigtran are protected by copyright.

For more information about this technology contact:

Digital Ventures
University of Washington
Phone: (206) 616-3451
Email: ldorsey@u.washington.edu