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Practical Innovation at BioCon 2003


Creating and Using Multi-protocol Bioinformatic Web Services
Jesus Castagnetto, Scripps Research Institute

Track: Techniques
Date: Thursday, February 06
Time: 11:30am - 12:15pm
Location: California Ballroom A & B

Since its inception in early 1998, the Metalloprotein-site Database and Browser (MDB) was designed to be a scientific resource for metalloprotein design and analysis, available to the research community, as well as providing quantitative data for our research as part of the Metalloprotein Structure and Design Program at The Scripps Research Institute. Users can access the MDB for interactive searching (e.g. zinc proteins with a resolution of up to 1.5 angstroms), and to perform analysis of data sets (e.g. distribution of Zn-His distances for 4-coordinate zinc).

In time, the need arose to allow other people, sites, and even programs to access this resource non-interactively, to include/embed data or analysis results seamlessly. This lead to the creation of a series of Web APIs that are exposed via a several Web services (HTTP-based, XML-RPC, and SOAP).

Castagnetto presents his experience creating multi-protocol Web services for the Metalloprotein Database and Browser, focusing on perfomance, reliability, and modularity. He emphasizes examples using more than one protocol when talking to a Web application as a strategy to improve inter-application performance. For example, making a SOAP RPC call to the MDB SOAP server to retrieve information on metal-binding sites, and then using the HTTP-based API to download programatically the corresponding structure files.

The MDB has made succesful use of open source resources (Apache, MySQL, PostgreSQL, PHP, Python), and its code, content, and data are covered by open source licenses.

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