institute for computational biomedicine: SigPath

CRT home > SigPath Project

[ description ]

SigPath is a collaborative project of the Institute for Computational Biomedicine and the Department of Physiology and Biophysics at the Weill Medical College of Cornell University, and the Department of Pharmacology & Biological Chemistry at Mount Sinai School of Medicine.

SigPath is an information system designed to support quantitative studies on the signaling pathways and networks of the cell. More

Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Quantitative information management for the biochemical computation of cellular networks. Science STKE. 2004 248:PL11. [PubMed], [Full Text]

Srdanovic M, Schenk U, Schwieger M and Campagne F. Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. BMC Bioinformatics. 2005. 6:5 [Abstract] [Full Text]

[ documentation ]

Some novel or noteworthy features of SigPath include:

Import of background information

Import information through XML submission

Full text search in background information

BioWizard for submission of binding interactions

BioWizard for submission of phosphorylation information

Assemble and export simple quantitative models

Exporting SigPath entities as XML

Reviewing data in SigPath

The following animated tutorials highlight some basic uses of SigPath:

Querying SigPath for interactions

Querying SigPath for small molecules

Querying SigPath for proteins

Submitting phosphorylation reactions into SigPath using the BioWizard

Submitting binding reactions into SigPath using the BioWizard

Sumbitting Interactions into SigPath via XML upload

Assembling a quantitative model using SigPath

Exporting a SigPath model for JSIM

Exporting a SigPath model for Kinetikit

Exporting a SigPath model in SBML format

Exporting a SigPath entity (models, reactions etc.) in XML format

Reviewing data in SigPath

[Note: To view the animated tutorials you need a Macromedia Flash Player. If your browser does not have a flash player plugin you can download it from the Macromedia web site]

Documentation for developers is provided on a separate page.

[contributing]

There are many ways in which you can contribute to SigPath. The simplest way is probably to contribute information to SigPath. We also look forward to feedback about the information system and the information it offers. If you are interested in contributing to the development of SigPath, please contact us, as we would like to start exploring ways of opening parts of the project to other research groups.

[ contacts ]

Please feel free to contact one of the members of the project for questions about SigPath. Questions related to bioinformatics and the design of the information system should be directed to Fabien Campagne, biological queries should be addressed to Ravi Iyengar and Harel Weinstein.

The SigPath mailing list provides a forum where future features can be requested and discussed.

We also maintain a bug tracker for the project. Specific problems with SigPath can be logged directly in our bug tracker [Mantis]. You can register as a user (prefered option, so that we can contact you to followup on the bug), or login as a guest (username=guest, password=guest).

[ availability ]

The production version of SigPath is available at http://icb.med.cornell.edu/services/sp-prod/sigpath/

You can also download the source code for SigPath here

Disclaimer: the data offered in the current version of the production release has not been reviewed thoroughly and contains known discrepancies with published data. This data is provided only as an illustration of SigPath and will be replaced with curated information as we progress with data entry and review.

If you are interested in SigPath, we suggest that you bookmark this page (SigPath Project). We will post announcements about the status of the application (planned maintenance, upgrades, etc) here and on the mailing list.

SigPath Production

SigPath Navigator

Project Overview

Contributing to Sigpath

SigPath News

Jul 25th, 2005; New SigPath beta release [Release info]
Feb 9th, 2005; New SigPath production release [Release info]
Dec 9-11th, 2004; The First SigPath workshop was held in New York City. [Workshop info]
Nov 3rd, 2004; New SigPath beta release [Release info]
Oct 29th, 2004; New SigPath production released [Release info]
Sep 22nd, 2004; New beta release of SigPath available for preview and testing. [Release info]
Sep 3rd, 2004; A description of SigPath is now available in Science STKE. SigPath users may now cite it as Quantitative information management for the biochemical computation of cellular networks. Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Science STKE 248:PL11. (2004). [SigPath]
Mar 2nd, 2004; A new release of SigPath is now available. [SigPath]
Mar 1st, 2004; SigPath is now released under the GNU General Public License [download source code]

[older news]

Events

Jul 7th; 1:00pm-2:00pm: Understanding Computation in Large Neuronal Networks - Yasser Roudi, Ph.D.; Nordic Institute for Theoretical Physics; LC-504 [Physiology and Biophysics Special Seminar]
Nov 1st: Sequencing of Individual Genomes: Impact on Society and Ethics ; Geneva, Switzerland [HUGO Symposium on Genomics and Ethics, Law and Society]