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[Chlamydomonas] The iPlant Collaborative: what potential does it have for advancing plant research?

Rich Jorgensen via chlamy%40net.bio.net (by raj from Ag.arizona.edu)
Sat Mar 15 14:40:55 EST 2008


Dear Chlamy researchers,

I'm writing to encourage creative thinkers in your community invest a =20=

little time in understanding the iPlant Collaborative =
(www.iplantcollaborative.org=20
) and thinking about what it might be able to do for the plant =20
sciences. To jumpstart your thinking process, you might want to =20
consider participating in the iPlant Collaborative's April kickoff =20
conference at Cold Spring Harbor Lab, either in person or via our =20
free, live webcast which will allow for direct participation (details =20=

at our web portal). Participation in the conference is NOT necessary =20
for participation in the Collaborative, but may be helpful in =20
understanding how best to participate. International participation is =20=

both welcome and encouraged.

The first principle of the iPlant Collaborative =96 our "prime =20
directive", one might say =96 is that it must be "by, for and of the =20
community". A second major principle is that the iPC's =20
cyberinfrastructure designs must be driven by specific, compelling, =20
and tractable Grand Challenges in the plant sciences. A third major =20
principle is that the Collaborative must serve the entire breadth of =20
the plant sciences, including ecology, evolution and organismic =20
biology as much as the molecular, cellular and developmental =20
disciplines, and via Grand Challenges integrated across the 'divide', =20=

from the molecular to the organismic to ecosystems. In order to ensure =20=

Collaborative resources are dedicated to the most compelling Grand =20
Challenges in the Plant Sciences, the best and the brightest in plant =20=

biology will need to invest time and provide leadership to ensure the =20=

field assembles and submits the best possible GC proposals to iPlant's =20=

external Board of Directors.

Importantly, the project is NOT  based on the idea of "if we build it, =20=

they will come." Rather, the community must FIRST come together and =20
decide WHAT we should build, or no cyberinfrastructure will actually =20
be built. So, the first challenge we face is to engage the community =20
and convince those of you who think deeply about the important =20
questions in plant biology, as well as comprehend the real, down-and-=20
dirty details of data quality, availability and analysis, to identify =20=

the most compelling and tractable Grand Challenges that require =20
computational approaches and cyberinfrastructure development. (see =20
iPlant's community wiki to contribute your discussion of what these =20
GC's ought to be.)

Self-forming Grand Challenge Teams are the most direct way to =20
participate in the iPlant Collaborative. Any group can start a Grand =20
Challenge Team, or propose a Grand Challenge Workshop at which to =20
develop one. GC Teams are central to the iPlant Collaborative because =20=

the community through its Board of Directors will choose which Grand =20
Challenges should be prioritized for cyberinfrastructure design and =20
development. Once GC Teams are chosen (our target is 2-4 GCT's before =20=

late 2008/early 2009), the iPC's Integrated Solutions Team, led by =20
Lincoln Stein (CSHL) and Sudha Ram (UA), will work with each GCT to =20
design a 'Discovery Environment' to address a particular grand =20
challenge. Successful development of these prototype =20
cyberinfrastructures (Discovery Environments) will require close =20
interaction between IS Team  and GC Team members. (See the Grand =20
Challenge Process tab at our web portal for more details.) We also =20
look forward to partnering with other CI efforts around the world.

Self-forming Grand Challenge Teams do not need to wait for the =20
conference in April to get started. The conference is an opportunity =20
for plant and computing researchers to get together and so attendance =20=

is one way to foster or participate in formation of GC Teams. It is =20
not obligatory for participation in the project (though we do hope to =20=

have broad representation of the full range of plant biologists and =20
computing researchers so that discussions will be high quality and =20
balanced).

The conference is NOT a bioinformatics meeting - it is a biology =20
conference aimed at defining which are the most compelling and =20
tractable grand challenges in the plant sciences that might benefit =20
from cyberinfrastructure development. The conference will be webcast =20
live, allowing for direct participation in discussions over the web =20
(and will be archived for later viewing). You can participate on your =20=

laptop. Another suggestion I would offer would be for interested =20
organizations to arrange a webcast location (requiring only a =20
computer, web access and a projector) where local researchers could =20
come together to participate in and discuss the conference - we will =20
have facilitators to ensure all persons can participate in discussion. =20=

Some institutions are also holding pre-meetings to discuss the =20
project: what it might mean for the campus and how to participate most =20=

effectively in the Grand Challenge identification process which will =20
define the direction of the project. I hope the community will =20
consider participating substantively so it will not be left out of the =20=

conversation, and so it will be positioned to participate prominently =20=

in the Collaborative as it develops. (Program and pre-registration =20
links for both in-person and virtual attendance are at the project's =20
web portal.)

To ensure community buy-in and ownership of the Collaborative, an =20
independent Board of Directors has been selected which will set =20
priorities for the allocation of Collaborative resources to particular =20=

grand challenges, through a process involving self-forming grand =20
challenge teams that will arise from the community and make proposals =20=

to the Board. The PI's will be available to facilitate the efforts of =20=

GC teams, but we are agnostic about which grand challenges should be =20
prioritized. To ensure substantial independence, the Board of =20
Directors was appointed through a bootstrapping process, via a =20
Nominating Committee, not by the PI's. One third of the Board will =20
refresh annually.

The composition of both the Board of Directors and the Nominating =20
Committee can be found at the project's web portal, =
www.iplantcollaborative.org=20
. To date, the Board includes biologists Rob Last (chair), Sabeeha =20
Merchant, Jim Birchler, Toby Kellogg, Jose Arguello, Susan Singer, =20
Russ Monson, David Rand, Jean-Philippe Vielle, and Mark Westoby. An =20
equal number of Board members represents the computing research =20
community, from bioinformatics to computational biology to computer =20
science, information science, and computing infrastructure (Eric =20
Mjolsness, Steve Mayo, Fran Berman, Gwen Jacobs, Laurie Kirsch, Mohan =20=

Tanniru), in order to be able to determine which proposals are really =20=

tractable and to advise and guide Collaborative management. Thus, the =20=

Board will possess diverse, balanced expertise with which to evaluate =20=

any Grand Challenge proposal submitted by the community.

The iPlant Collaborative is funded by NSF's Plant Sciences =20
Cyberinfrastructure Collaborative program in the Emerging Frontiers =20
division of BIO, as a $50M grant over 5 years to develop a =20
cyberinfrastructure for the plant sciences, from molecules, genes, and =20=

cells to organisms, ecosystems and evolution. As plant biologists, we =20=

are quite fortunate that our community has been given this unique =20
opportunity to lead biology cyberinfrastructure development in the =20
service of trying to solve biology=92s major, unanswered questions. The =20=

reason the plant biology community has been entrusted with this =20
opportunity and responsibility is, I believe, because we have shown =20
exceptional openness, creativity and leadership across disciplines and =20=

experimental organisms over many years. What better community than =20
plant scientists could NSF have chosen for this program? Also, had it =20=

not been the plant sciences, these funds would presumably have gone =20
instead to areas of biology other than plant biology. So, this is an =20
extraordinary opportunity for the whole community, and one that we can =20=

all feel proud to have earned.

Feel free to pass this letter along to your colleagues. I look forward =20=

to seeing many of you at CSHL, either online or in person, for what I =20=

believe promises to be a pivotal event for plant biology. We are able =20=

to waive onsite costs to increase diversity in the conference, so =20
please don't hesitate to ask if you feel you are in that category =20
(flexibly defined).

More information can be found at www.iplantcollaborative.org, =20
including the NSF solicitation, our proposal, site visit questions and =20=

answers, a ppt presentation, and other documents, as well as 1-2 page =20=

backgrounders on different aspects of the project. I am available any =20=

time to discuss the project.

Rich Jorgensen

Director, The iPlant Collaborative

www.iplantcollaborative.org





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