We have extended the SigPath ontology and XML data exchange format to represent reactions with custom kinetics.

A new BioWizard was implemented to support custom kinetics. When users assemble reactions with this BioWizard, they can now either define a new kinetics, or use kinetics already submitted to SigPath (e.g. Mass-action and kinetics defined by other users).

SigPath Navigator is a desktop application designed to connect to multiple SigPath instances accross the internet, to retrieve and visualize connections between SigPath entities (i.e., molecules, reactions, etc). This new beta release of SigPath Navigator has all the functionalities of the previous version, plus many new features as listed below:

Retrieval of all types of entities supported by SigPath- basic and enzymatic reactions, named chemical interactions, pathways, and models.

Retrieval of backward references, or in other words, the set of entities that reference the entity the user has selected. For instance, the backward references of a molecule include all the reactions that directly include this molecule. The backward references of a reaction include models and pathways that use this reaction. Forward references (e.g., reaction -> molecules) are fully supported as well.

Assembly and submission of pathways. This allow users to obtain reactions from a SigPath entity, to create a pathway graphically with the Navigator, and to submit this pathway to a SigPath instance.

Entities selected in the Navigator can be saved as XML in the SigPath XML exchange format. In the navigator, the user can adjust the graph of entities at will before creating the document. This complements the XML download options offered in SigPath and helps transfer subsets of information from one SigPath instance to another.

Two viewing options (compact and expand) display links between entities in different ways.

It is now possible to clear the drawing area to start a new navigation.

[For developers]

The current release of SigPath Navigator combines the use of Document-style web services and Castor to handle transfer of SigPath entities from one instance to another. Castor is an XML data binding package that provides mapping from XML-schema to Java objects, and this framework has been in place since the very early versions of SigPath. Integrating Document-style web services with Castor has the following advantages: 1) Java objects that are mapped to the SigPath schema can be re-used by the Navigator; 2) SigPath entities that are transferred across multiple instances using the Navigator can be validated by the same set of rules that the instances use for validating uploaded XML files.

[Download]

Code snapshots of the new beta release can be downloaded from:

SigPath Source Code: beta_20050719112114.zip [18 MB, July 19th 2005]

Detailed installation instructions: [HTML] [PDF]

This new version is offered as a preview of new features and should be used for testing purposes only. Data submitted to this release will be discarded when the code is released in production mode; furthermore, the spids (SigPath identifiers) of named chemicals and their interactions may change between the beta release and the production version.

We are aware of a few minor bugs with this beta version. These bugs are listed in the project [Mantis] bug tracker. We are working to resolve these issues before deploying this version as a production instance of SigPath. 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.