August 2006
Trends and Tools in Bioinformatics and Computational Biology
Rick Stevens, Associate Laboratory Director, Computing and Life Sciences – Argonne National Laboratory, Professor, Computer Science Department – The University of Chicago

Are grids really being used that much for real biology?

There are several national and international projects developing grid infrastructures for biological research. Many of these projects are loosely affiliated by sharing services and technology, and all are working towards a vision of a BioGrid. Several are worth looking at.
The TeraGrid is sponsoring two Science Gateways for Biology; one developed by RENCI, Biology and Biomedical Science Gateway Renaissance Computing Institute, UNC;11 and one developed by the University of Chicago.12 Both of the TeraGrid gateways are aimed at enabling communities to leverage the TeraGrid computing and data resources without a need for obtaining a dedicated allocation of resources. They are examples of an emerging concept of "community allocations," which are aimed at lowering the adoption barrier to cyberinfrastructure. The Open Science Grid also hosts biological applications such as the GADU virtual organization.13 In Europe, one of the most well developed Life Sciences grid projects is MyGrid.14 MyGrid is developing a comprehensive set of web services based tools and services.

There is a lot of talk about web services as a future direction for the Internet. How will web services impact biology?

Web services are the key to providing the ability for groups around the world to collaborate on building new tools that leverage each other’s data and computational services without prior coordination. Early web services deployments in life science suffered from poor implementations, poor performance and lack of high-quality data. More recent efforts are dramatically improving. The KEGG group in Japan recently published a comprehensive set of web services15 for accessing their data, which have proven to be robust and of moderate performance. I’ve used these services routinely for the last year and find them simple, yet useful. As web services interfaces become more common, it will be possible for many groups to build applications that leverage the major data sources. This is one of the most important trends, but it is still far from being generally demonstrated.

Are there systems in use today that leverage web services?

One system worth exploring is Taverna.16 Taverna is a collaboration between the European Bioinformatics Institute (EBI), IT Innovation, the School of Computer Science at the University of Newcastle, Newcastle Centre for Life, School of Computer Science at the University of Manchester, and the Nottingham University Mixed Reality Lab. Additional development effort has come from the Biomoby project, Seqhound, Biomart and various individuals across the planet. Development is coordinated through the facilities provided by SourceForge.net and predominantly driven by the requirements of biologists in the UK life science community. Taverna enables end users to compose bioinformatics web services in a graphical environment for computing novel workflows.
Is industry developing any new cyberinfrastructure tools that might alter the landscape in biology?

It is likely that several of the commercial search engine companies (e.g. Google and Microsoft) will explore the issue of coupling biological searches of open literature and databases with computational services with access to commercial tools and databases. These tools will most likely be emerging examples of coupling commercial tools (web services infrastructure, indexing and search technologies) with the best of the open science literature.

Pages: 1 2 3 4 5

Reference this article
Stevens, R. "Trends in Cyberinfrastructure for Bioinformatics and Computational Biology," CTWatch Quarterly, Volume 2, Number 3, August 2006. http://www.ctwatch.org/quarterly/articles/2006/08/trends-in-cyberinfrastructure-for-bioinformatics-and-computational-biology/

Any opinions expressed on this site belong to their respective authors and are not necessarily shared by the sponsoring institutions or the National Science Foundation (NSF).

Any trademarks or trade names, registered or otherwise, that appear on this site are the property of their respective owners and, unless noted, do not represent endorsement by the editors, publishers, sponsoring institutions, the National Science Foundation, or any other member of the CTWatch team.

No guarantee is granted by CTWatch that information appearing in articles published by the Quarterly or appearing in the Blog is complete or accurate. Information on this site is not intended for commercial purposes.