NYU Bioinformatics Lab Courant Institute of Mathematical Sciences

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 NYUSIM database.

Simpathica has been built within the scope of our project Algorithmic Tools and Computational Frameworks for Cell Informatics.

Related Projects.

There are a few projects related to Simpathica.

  • NYUSIM (part of NYUMAD) is a database that stores simulation traces.
  • Query Maker Online is a web based interface to our Natural Language Temporal Logic Query system. It uses NYUSIM and it is meant to be a simple showcase of Simpathica/XSSYS capabilities.

Downloadable Packages

The following packages are available for download as our group's submission for the upcoming BioSpice release (expected third quarter 2004.)

  • Simpathica (2004-07-18 release)
    The Simpathica application, comprising a SBML-enabled pathway editor, an Octave OAA agent and the XSSYS Temporal Logic Query subsystem with a Natural language Interface.
  • Simpathica Netbean (2004-01-31 release)
    A preliminary Netbean that allows to start Simpathica from a BioSPICE Dashboard work-flow.
  • NYU MAD OAA2 Client (.jar) (2003-05-01 release)
    A simple OAA client to interact with the NYUMAD database (to be updated by November 30th, 2003.)
  • NYUMAD (2003-11-07 release)
    The NYUMAD microarray database: a database capable of storing micro-array data and to export MAGE-ML data.
  • NYUSIM Client (2003-11-07 release)
    The NYU Simulation Trace database: a database capable of storing simulation traces in the format specified by BioSpice.
  • NYU Biowave (2003-05-01 release)
    A simple simulation trace clustering tool.

Simpathica/XSSYS

Here you can download the standalone Simpathica/XSSYS Temporal Logic Trace Analysis system. The latest release contains the capability of formulating queries about multiple traces, and improvements to the integrated Natural Language Interface.

  • Windows (2004-07-16 release.)
  • Linux (2004-07-17 release.)
    Note: there may be dependencies on the Motif version installed on your machine.
  • Mac OS X upcoming.

Simpathica/XSSYS OAA Agent

Here you can download the OAA Agent wrapping the Simpathica/XSSYS Temporal Logic Trace Analysis system.

  • Simpathica XSSYS OAA Agent (2004-07-16 release)
    The Temporal Logic analysis component of Simpathica, unbundled for BioSpice Dashboard integration.