A new production release of SigPath is now available.

This new release offers new features and many bug fixes. Major new features include:

For users:

Ability to manage interactions when a limited amount of information exists about the pair of molecules that interact. The SigPath ontology has been extended to represent NamedChemicals, molecules that are only represented by name, and NamedChemicalInteractions, that describe interactions about these molecules.

Interactions between nuclear receptors and other molecules have been obtained from [1] and submitted to this instance of SigPath. This dataset helps show how SigPath can be used to search and navigate such large-scale datasets. An example of visualization is given in the figure (the images are clickable in SigPath)

Support for multi-compartment models has been added. Multi-compartment models can be added as SigPath XML submissions. A future release will provide a user interface to submit multi-compartment models.

A new SBML export page allows the export of models in any of the three major SBML versions: Level 1 version1, Level 1 version 2, Level 2 version 1. This increases interoperability between SigPath and the modeling environments that support of the version of SBML. The page supports a new option to export a diagram of the model in the proposed SBML diagram extension. This page can be found on the view model page for each model (click "export to SBML") [Example].

Background information has been upgraded. This version of SigPath is built with SwissProt v44 and a subset of TrEMBL v27 (427,879 proteins).

For developers:

This is the first version of SigPath to use the Lucene text indexer. This release makes it possible to compare the performance of Lucene with the SigPath JDO text indexer.

This is also the first formal release of SigPath to use the Tapestry web framework. The submit named chemical page (linked from the main page when the user is logged in) demonstrates how tapestry integrates with Struts in the SigPath application.

code snapshots of the new production release can be downloaded from:

SigPath Source Code: beta_20040920164127.zip [17 MB, 20th September 2004]

Detailed installation instructions: [HTML] [PDF]

Please submit reports of specific problems or feature requests directly in our bug tracker, or email us your feedback to icb@cornell.

The SigPath Team.

[1] Sylvie Albert, Sylvain Gaudan, Heidrun Knigge, Andreas Raetsch, Asuncion Delgado, Bettina Huhse, Harald Kirsch, Michael Albers, Dietrich Rebholz-Schuhmann, Manfred Koegl Computer-assisted generation of a protein-interaction database for nuclear receptors. Mol Endocrinol. 2003 Aug; 17 (8): 1555-67.] [PubMed]