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SDSC Releases Developer Preview of Collaboration Notebook Framework


The San Diego Supercomputer Center has released a preliminary version of an application that promises to address a number of data-management challenges in bioinformatics and other scientific disciplines.

The application, called the Collaboration Notebook, sprang from SDSC's Encyclopedia of Life — an ambitious project that aims to catalog the complete proteome of every living species. Greg Quinn, principal investigator at SDSC, said that he and his co-developers soon realized that the software, originally called the EOL Notebook, would be of interest to other bioinformatics projects and possibly other research domains.

Quinn said that the application is essentially a "developer's framework" that enables developers to easily write "smart clients" to store, access, and share large amounts of data.

The "smart client" is a dedicated application that runs on a user's PC, unlike so-called "thin clients" such as web browsers, which offer limited capability for scientific data management, Quinn said. According to the project's website, the advantage of the smart client paradigm "is that the application can understand the information/data which it handles, and because it is a dedicated application, it can provide a much rich[er] user interface than is possible with a web browser."

Quinn said that the system will work with any data for which there is a "naming scheme or an ontology," and that it could serve as an effective front end for web services-based bioinformatics integration tools like BioMoby.

A "developer preview" of the application is available for download at, and Quinn said that some documentation and a "fairly crude" user manual are available. The current version includes a demonstration interface that enables users to run a Blast search against a number of different data sources.

Future development of the notebook will be determined by funding, Quinn said. The first phase of the project was funded by Microsoft Research as a means of demonstrating "the full power of the Windows operating system," Quinn said. The SDSC team now plans to apply for federal grants "with a view to making it a multi-platform system."

SDSC is hosting a one-day developer workshop in early 2006 for bioinformatics developers and other scientific IT specialists interested in learning more about the notebook's capabilities.

The notebook is freely available for those using it for educational, research, and non-profit purposes. Those interested in using it for commercial purposes or incorporating it into commercial tools will require a license from the UCSD tech transfer office.

— Bernadette Toner ([email protected])

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