institute for computational biomedicine: SigPath

SigPath information for developers

See the project JavaDocs and the source download page. Our icbtools server offers other developer resources (some may be visible only from within Weill Cornell).

Submissions to SigPath in XML format need to adhere to the SigPath Submission XML Schema therefore, we also maintain an annotated XML schema documentation.

We test SigPath both with unit tests (JUnit) and system level tests. We are using Clover to visualize to what extent the code of the project is tested by these series of tests. Test coverage metric reports are generated by Clover, and updated as part of the cruisecontrol continuous integration builds. Such reports are created with the automatic project builds and published on the web. Historical views show how coverage evolves from build to build.

The SigPath ontology is based on the EcoCyc ontology (as described in [Karp00]). We have adapted this ontology to an JDO-compliant object-oriented database management system. The SigPath ontology has further evolved to represent quantitative information about signaling pathway components and respond to evolutions of the SigPath project.

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SigPath Production

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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

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301