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Please visit the Web Services User Forum (WSUF) for the latest news and discussions.
Our goal is to provide transparent access to biomedical applications such as APBS, GAMESS, etc. on distributed computational resources. Multiple users may interact with these applications simultaneously via a variety of interfaces – Web-based portals (e.g. the NBCR portal), rich interfaces such as the Python Molecular Viewer (PMV) or the Mozilla-based Gemstone framework, or a workflow framework such as Kepler. Furthermore, complex biomedical analysis pipelines or workflows will be composed from these applications.
We are developing a service-oriented architecture that wraps biomedical applications as Web services. These services are capable of serving multiple client requests concurrently. Additionally, since Web services are language and platform agnostic, they are easily accessible by clients written in different languages on disparate platforms. Ideally, all our Web services will have inputs and outputs defined in great detail using XML schemas. This enables easy validation of inputs and stronger datatyping, and also enables generic Web service workflow tools to compose these services easily. This is generally a big improvement over traditional methods that are error-prone and non-generic, where application-specific scripts need to be written to parse and translate between monolithic flat file-based inputs and outputs in order to link multiple applications. However, in some cases, for rapid prototyping we also use Web services that are less strongly typed, but automatically generated and deployed, via the Opal toolkit.
For more details about our architecture, you are encouraged to look at our Publications, and Presentations.
The Opal toolkit has been used to deploy several scientific applications as Web services, such as Babel, PDB2PQR, QMview, PSize, MEME, LigPrep, etc. The APBS and GAMESS services have been handwritten for better type validation and greater flexibility.
View a complete listing of scientific services running on ws.nbcr.net, pebbles.nbcr.net, or apbs.nbcr.net.
| Client | Description | ||
| Gemstone | Many of the web servcies developed using the Opal toolkit is available in the Gemstone application. The installation is simple, and it’s a lightweight plugin to the Mozilla Firefox browser. | ||
| PMV | The Python Molecular Viewer uses the Opal toolkit to access Viper database and APBS web services hosted by NBCR. | ||
| Kepler | The Kepler workflow management software distributes Opal web servcie based workflow examples which couple MEME and MAST based web services. | ||
| My WorkSphere | The NBCR portal uses Opal toolkit to expose applications such as MEME as portlets quickly | ||
Opal: Simple Web Services Wrappers for Scientific Applications. Sriram Krishnan, Brent Stearn, Karan Bhatia, Kim K. Baldridge, Wilfred Li, and Peter Arzberger. SDSC Technical Report TR-2006-5, 2006.
An End-to-end Web Services-based Infrastructure for Biomedical Applications. Sriram Krishnan, Kim Baldridge, Jerry Greenberg, Brent Stearn, and Karan Bhatia. In proceedings of Grid2005, 6th IEEE/ACM International Workshop on Grid Computing, November 2005 (pdf).
Web Services-based Data Integration for Life Science Computations. Sriram Krishnan, Brent Stearn, Karan Bhatia, Jerry Greenberg, Wilfred Li, Peter Arzberger, and Kim Baldridge. SDSC Technical Report TR-2005-2, 2005.
Opal: Wrapping Scientific Applications as Web Services Sriram Krishnan, et al. NBCR Special Seminar, SDSC, February 2006: pdf.
An End-to-End Web Services-based Infrastructure for Biomedical Applications. Sriram Krishnan, et al. Grid2005, 6th IEEE/ACM International Workshop on Grid Computing, November 2005: pdf.
GSI-based Security for Web Services. Sriram Krishnan. GEON Meeting, June 2005: pdf.
A Web Service Based Architecture for Biomedical Applications. Sriram Krishnan, et al. International Symposium on Web Services for Computational Biology and Bioinformatics, Blacksburg, VA. May 2005: pdf.
For more information and any questions, comments or other feedback, feel free to contact Sriram Krishnan [Note that the email address is spam-proofed], or post to the Web Services User Forum (WSUF).