[Arabidopsis] Planning for future home of Arabidopsis bioinformatics

Joanna Friesner via arab-gen%40net.bio.net (by jdfriesner from ucdavis.edu)
Wed Sep 7 22:08:46 EST 2011


Dear Arabidopsis community,

The Steering Committee of the recently-formed International Arabidopsis
Informatics Consortium (IAIC, definition below) is developing a Design
Workshop which is envisioned as a 2.5 day event with discussions facilitated
by a professional moderator. The purpose of the Design Workshop is to bring
together individuals to discuss the format and capabilities that the future
Arabidopsis Informatics Portal (AIP, definition below) should have. It is
anticipated that the AIP will partially rely on functionalities developed
over the last few years by the iPlant Collaborative (iPC). iPC is an
NSF-funded project to develop cyberinfastructure and computational tools for
plant science.

Due to logistical constraints, the Workshop will be limited to about 30 key
participants as described below. However, the Steering Committee welcomes
and solicits input from the broader community and is looking into various
ways for additional community participation which will be updated on the
IAIC website as they unfold. See 'Providing Input' below as well.

Workshop attendees are expected to fill various roles including, but not
limited to:
(1) Cyberinfrastructure and Bioinformatics experts- those with the technical
knowledge to develop the AIP and facilitate interactions with external
bioinformatics resources.
(2) 'Representative Users'- major data generators to include users from a
variety of communities and research areas that can provide examples and
'test cases' of current and future bioinformatic needs, challenges, and
approaches.
(3) 'Lead Users'- individuals (in computing especially) that are
forward-thinking about future computing requirements and challenges.
(4) Provocateurs'- individuals that can assist by challenging the thinking
of other attendees and act as 'devil's advocates.' These individuals will
likely be from outside the Arabidopsis basic research community to provide
different perspectives (e.g. industry and other organismal database
experts).
(5) Agency Observers- key members of funding agencies from major countries
supporting Arabidopsis research (e.g. USA, UK, Germany, etc) who are
invested in supporting plant research now and into the future. Their
financial support is absolutely vital to the long-term sustainability of
Arabidopsis resources.

Expected Outcomes of the Design Workshop:
(1) one or a couple of teams of investigators ready to submit a proposal to
prototype the AIP to the NSF or other funding agencies, with coordination
across borders for international co-submission, if possible. 
(2) preliminary guidelines for community members wishing to develop core
components (or 'modules') that will link to the AIP (defined below.)
(3) guidelines for the IAIC Scientific Advisory Board (SAB, defined below),
that is expected to be formed by Spring, 2012 and will be critical to
advising progression of the IAIC.
(4) input to relevant funding agencies on community needs especially with
respect to funding aspects of the IAIC (e.g. AIP and modules.)

Providing Input:
If community members wish to provide input to the Steering Committee
regarding the Design Workshop (which is planned for Dec. 11-14, 2011), or
any other related matter, please email the IAIC
(arabidopsisinformatics from gmail.com) or by clicking the 'Email the IAIC' link
near the bottom of the preliminary webpage:
http://arabidopsis.org/portals/masc/IAIC.jsp

Definitions used:
IAIC - International Arabidopsis Informatics Consortium. These are the
contributors to core and non-core resources. The IAIC director is yet to be
named, to be elected by the IAIC based on recommendations from the SAB. The
interim IAIC director is Blake Meyers. The IAIC Steering Committee consists
of members on the NSF RCN (Award Number: 1062348): PI Blake Meyers,
University of Delaware, Co-PIs Erich Grotewold (Ohio State University),
Doreen Ware (CSHL), Jim Carrington (Danforth Center), Volker Brendel (Iowa
State University), and other senior personnel: Nicholas Provart (University
of Toronto, Canada), Dan Stanzione and Rion Dooley (UT-Austin/iPC); Ruth
Bastow (GARNet, UK), and Jim Beynon (University of Warwick, UK). The IAIC
itself extends to the larger community  and includes investigators (from any
nation) contributing Arabidopsis modules and resources.
 
AIP - Arabidopsis Informatics Portal. The primary interface providing
dynamic access to core resources and key non-core resources, and links to
"boutique databases". This is yet to be formed or funded, but will be a
critical resource to be funded competitively in one or more of the nations
with a significant Arabidopsis scientific presence. This will act as the
central hub for coordination of Arabidopsis informatics, and will define
standards for data storage and access and interconnectivity.

Core component - Module essential for the functioning of the IAIC including
the central portal, the "gold standard" genome, literature curation, and
stock center resources; currently provided in part by TAIR.

Non-core component - Module identified by the IAIC as an essential component
once the core modules are in place; the definition of core/non-core is
dynamic and will depend on the community needs.

Boutique databases - Resources developed for lab-specific projects that may
be of significance to a small group of researchers, but still should be
accessible from the AIP, perhaps as links if the data are not formatted
according to AIP standards.

SAB - Scientific Advisory Board. Yet to be named; a group of seven
international scientists that will actively oversee the IAIC and its
activities. Selection will involve input by the Multinational Arabidopsis
Steering Committee (MASC).

Resources:
IAIC RCN Proposal: original text can be found:
(http://arabidopsis.org/portals/masc/IAIC_RCN_Aug2010.pdf).
The Plant Cell Commentary Publication on establishing the IAIC:
(http://www.plantcell.org/cgi/reprint/tpc.110.078519v2)

With best regards,
Joanna Friesner
Coordinator of the North American Arabidopsis Steering Committee (NAASC)



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