[CAnet - news] Cyber-Infrastructure for Biology and Life Sciences

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[This month's issue of Cyberinfrastructure Technology Watch Quarterly has an
excellent article by Rick Stevens, Associate Lab Director for Computing and
Life Sciences at Argonne National Laboratory on the use of
cyber-infrastructure (CI) for bio-informatics and life science applications
in general  especially in the use of web services.  Some people see CI as a
tool for centralizing the administration, control and distribution of data
from the instruments all the way through to the petascale systems.  But as
Rick Stevens points out, web services, one of the key components of CI
enables scientists from around the world "to collaborate on building new
tools that leverage each other's data and computational services without
prior coordination". Workflow tools like Taverna, Keppler, BPEL, etc allow
researchers to link and combine data from disparate sources to investigate
new possibilities.  Some excerpts from the original article  -- BSA]

http://www.ctwatch.org/quarterly/articles/2006/08/trends-in-cyberinfrastruct
ure-for-bioinformatics-and-computational-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.

One system worth exploring is Taverna. 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.


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.


Please visit http://www.ctwatch.org/quarterly/ at your convenience to get
your own copy of this issue of CTWatch Quarterly.  

For our November issue, guest editor Jeremy Kepner of the MIT Lincoln
Laboratory, who leads the DARPA HPCS Productivity Team, will present a
collection of articles that details the efforts within the DARPA High
Productivity Computing Systems program. We expect that our November issue
will be a double issue that covers the gamut from HPC software development
to HPC architecture and benchmarking and will highlight current problems as
well as new challenges for the future.

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These news items and comments are mine alone and do not necessarily reflect
those  of the CANARIE board or management.


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