This new release offers several key new features, including:

For users:

A new set of user interfaces to assemble models and edit them after the first submission.

On the fly validation of models while creating or editing them. Model validation occurs everytime the user changes data in a model.

Support for models with several compartments (multi-compartment models). The model assembly user interface let users add new compartments to a model. Changes to the compartments after the model has been created are also supported.

Model compartments can be defined with a name, a description and information about which other compartments the new compartment is in contact with (e.g., a cytosol compartment would be defined in contact with a nucleus compartment). Compartments can also include other compartments, in a hiearachical way, so that the entire cell compartment can be defined as including the cytosol, which itself may include the nucleus compartment.

Concentrations of chemicals involved in reactions that participate in models are defined globally for the model (i.e., total concentration of chemical in a model), and also locally at the level of each compartment (i.e., initial concentration in a compartment is defined as a fraction of the initial total concentration).

Support for excluded reactions. More details about this advanced features will be provided online.

Model snapshots. Editing a model which already existed in SigPath results in creating a new model instance, a model snapshot. The snapshot is given a new SigPath identifier, and is linked to the original model. The original model is unchanged by the edit, and the new snapshot harbors the changed data. This mechanism provides a first approach to maintaining versions of models. For instance, model [HTML] is a snapshot of the original MAPK model [HTML].

First public release of the SigPath Navigator. This desktop application is designed to connect to various SigPath instances accross the internet, retrieve information and look at connections between SigPath entities (i.e., reactions, molecules, models, etc). This version is really mostly a technology testbed, but has a few features that may used now.

For developers:

This release provides many examples (model creation and editing UI) of the use of the Tapestry web framework to create SigPath user interfaces.

The new model user interface code demonstrates how changes to a model are validated before committing the changes to the database. This procedure uses the xml import validation tools which are also used for XML submission. A key property of this procedure is thus that SigPath uses the same validation rules for XML submission and data modifications through the user interface. The validation mechanism implemented in the XML submission components supports both syntactic and semantic validation rules.

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

SigPath Source Code: sigpath_20041103182759.zip [22 MB, November 3rd 2004]

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.