DARPA BioComp Program 2001-2004

Algorithmic Tools and Computational Frameworks for Cell Informatics

Tools for modeling cellular, inter-cellular and genomic processes with specific applications to understanding signal transduction among cancer cells.

Principal Investigator: Bud Mishra

Collaborator: Mike Wigler, CSHL

People

• Marco Antoniotti, NYU
• Paolo Barbano, NYU (and Dept. of Mathematics, Yale)
• Jiawu Feng, NYU
• Marc Rejali, NYU
• Archisman Rudra, NYU
• Marina Spivak, NYU
• Nadia Ugel, NYU

Objective

The central claim of this proposal is that, by drawing upon mathematical approaches developed in the context of dynamical systems, kinetic analysis, computational theory and logic, it is possible to create powerful simulation, analysis and reasoning tools for working biologists to be used in deciphering existing data, devising new experiments and ultimately, understanding functional properties of genomes, proteomes, cells, organs and organisms.

Projects and Systems

Simpathica

Simpathica is a set of tools capable of simulating and analyzing biological pathways. It consists of a front end and a back end. The front end is a pathway editor which generates a set of Ordinary Differential Equations, which are in turn simulated using Octave. The back end, also known as XSSYS, is a temporal logic analysis tool which can answer queries about the time course behavior of a set of pathways. A recent addendum to the XSSYS back-end is a Natural Language Interrogation interface that can be used in lieu of the pure Temporal Logic Query system.

The infrastructure of Simpathica is based on the OAA architecture from SRI and on the NYU BioSim database.

Simpathica components can be downloaded from our Software page.

NYU MAD

• Built-in collaborative architecture to manage experiments run by geographically distributed groups.
• Integrated statistical analysis tools to manipulate gene expression experiments of various complexity.

NYU SIM

NYU BioWave