[Arabidopsis] Arabidopsis Web Services Demonstration Project

Town, Christopher D. cdtown at tigr.ORG
Tue May 23 07:52:17 EST 2006


Dear Colleagues

This message is to alert you to the activities of the ongoing
Arabidopsis Web Services Demonstration Project that was initiated in
response to the need perceived by the Mulitnational Arabidopsis Steering
Committee (MASC) for greater data integration within the international
Arabidopsis community. A web site describing this effort has been set up
at http://bioinfo.mpiz-koeln.mpg.de/araws and will be developed as the
project progresses.
A workshop attended by users, developers and database managers was held
at TIGR in April 2005 to explore the issues and develop a course of
action. At the workshop there was strong support for development of web
services as a complement to data warehouses such as TAIR, NASC and MIPS.
The recommendations of the workshop and an overview of how web services
would enhance data integration were included in last year's MASC report
and can also be found at
http://www.arabidopsis.org/info/2010_projects/TIGRDataWorkshop.pdf.
Following on from the TIGR meeting, an informational workshop was held
at the Arabidopsis Conference in Madison to introduce web services
concepts to the community. At the same time, the recommendations of the
TIGR meeting and end-user interest demonstrated at the Madison workshop
were communicated to the MASC committee and to members of the funding
agencies present at the MASC meeting. As a result of these activities
and subsequent proposal development in Germany (by Heiko Schoof, MPIZ)
and in the US (by Chris Town, TIGR) a pair of pilot projects have been
funded by the DFG and NSF respectively to implement a limited set of
Arabidopsis web services and to pave the way for broader community
involvement in web services development and utilization. 
Under the auspices of the project, two developers' workshops have been
held so far: one at MPIZ-Cologne in March and one at TIGR in April. Each
workshop was attended by 8-10 invitees that were selected to represent
some of the types of data that were amenable to web services deployment
and that would be valuable to the community. Instruction at the
workshops was provided by individuals with working experience of BioMoby
acquired through the PlaNet project (URL) or by other means. Workshop
participants were shown how to develop and deploy simple web services in
both Perl and Java and each ultimately opted for their preferred
programming modality. In addition to implementing test services within
the workshop IT environment, some participants were also able to set up
simple web services hosting their own data from their home institution
web servers and databases. Others began to implement their own web
services shortly after returning to their home institutions. Over the
course of the workshops, an increasingly detailed set of "how to" pages
that are intended to guide programmers new to web services in setting up
their own working environments were developed and reality tested. Sample
code and documentation can be found at
http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/. More
detailed step-by-step documentation including descriptions of the IT
requirements for hosting web services can be found at
https://biomoby.tigr.org/wiki/index.php/Main_Page). Reports of each of
the workshops will be posted to the ARAWS web site shortly.
Although these two workshops were, for logistical purposes, small and by
invitation, the long-term goal of the project is to be as open and
inclusive as possible. It is hoped that the "how to" pages referenced
above will go a long way towards guiding the more technology savvy
individuals through the web services development process. Each of the
project centers (MPIZ and TIGR) has a bioinformatician dedicated to the
project who can provide e-mail or phone consultation on specific
projects and in a limited number of instances will be able to visit a
client site to advise and assist in web services deployment. 
At the upcoming Arabidopsis meeting in Madison, the project will be
holding a workshop with several goals in mind:
1. Overviews of web services concepts and implementation, including
workflows;
2. Brief talks on web services developed during this project;
3. Solicitation of community input on desirable web services and
workflows - use cases.

There will also be opportunities for one-on-one discussions and
demonstrations at the web services poster.

Please feel free to contact either of the project leaders with questions
or comments. We hope that you will visit the web sites and look over the
materials there. We look forward to demonstrating and discussing web
services with the community at the Madison conference next month.

Best wishes

Heiko Schoof and Chris Town
__________________________________
Chris Town
Associate Investigator
The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD 20850

Office Phone: 301-795-7523
To page me at TIGR: 301-795-7000
Fax: 301-838-0208
Home Phone: 301-990-0878
Cell Phone: 301-204-6300



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