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

[Rich Jorgensen]

Dear Chlamy researchers,

I'm writing to encourage creative thinkers in your community invest a  
little time in understanding the iPlant Collaborative (www.iplantcollaborative.org
) and thinking about what it might be able to do for the plant  
sciences. To jumpstart your thinking process, you might want to  
consider participating in the iPlant Collaborative's April kickoff  
conference at Cold Spring Harbor Lab, either in person or via our  
free, live webcast which will allow for direct participation (details  
at our web portal). Participation in the conference is NOT necessary  
for participation in the Collaborative, but may be helpful in  
understanding how best to participate. International participation is  
both welcome and encouraged.

The first principle of the iPlant Collaborative – our "prime  
directive", one might say – is that it must be "by, for and of the  
community". A second major principle is that the iPC's  
cyberinfrastructure designs must be driven by specific, compelling,  
and tractable Grand Challenges in the plant sciences. A third major  
principle is that the Collaborative must serve the entire breadth of  
the plant sciences, including ecology, evolution and organismic  
biology as much as the molecular, cellular and developmental  
disciplines, and via Grand Challenges integrated across the 'divide',  
from the molecular to the organismic to ecosystems. In order to ensure  
Collaborative resources are dedicated to the most compelling Grand  
Challenges in the Plant Sciences, the best and the brightest in plant  
biology will need to invest time and provide leadership to ensure the  
field assembles and submits the best possible GC proposals to iPlant's  
external Board of Directors.

Importantly, the project is NOT  based on the idea of "if we build it,  
they will come." Rather, the community must FIRST come together and  
decide WHAT we should build, or no cyberinfrastructure will actually  
be built. So, the first challenge we face is to engage the community  
and convince those of you who think deeply about the important  
questions in plant biology, as well as comprehend the real, down-and-
dirty details of data quality, availability and analysis, to identify  
the most compelling and tractable Grand Challenges that require  
computational approaches and cyberinfrastructure development. (see  
iPlant's community wiki to contribute your discussion of what these  
GC's ought to be.)

Self-forming Grand Challenge Teams are the most direct way to  
participate in the iPlant Collaborative. Any group can start a Grand  
Challenge Team, or propose a Grand Challenge Workshop at which to  
develop one. GC Teams are central to the iPlant Collaborative because  
the community through its Board of Directors will choose which Grand  
Challenges should be prioritized for cyberinfrastructure design and  
development. Once GC Teams are chosen (our target is 2-4 GCT's before  
late 2008/early 2009), the iPC's Integrated Solutions Team, led by  
Lincoln Stein (CSHL) and Sudha Ram (UA), will work with each GCT to  
design a 'Discovery Environment' to address a particular grand  
challenge. Successful development of these prototype  
cyberinfrastructures (Discovery Environments) will require close  
interaction between IS Team  and GC Team members. (See the Grand  
Challenge Process tab at our web portal for more details.) We also  
look forward to partnering with other CI efforts around the world.

Self-forming Grand Challenge Teams do not need to wait for the  
conference in April to get started. The conference is an opportunity  
for plant and computing researchers to get together and so attendance  
is one way to foster or participate in formation of GC Teams. It is  
not obligatory for participation in the project (though we do hope to  
have broad representation of the full range of plant biologists and  
computing researchers so that discussions will be high quality and  
balanced).

The conference is NOT a bioinformatics meeting - it is a biology  
conference aimed at defining which are the most compelling and  
tractable grand challenges in the plant sciences that might benefit  
from cyberinfrastructure development. The conference will be webcast  
live, allowing for direct participation in discussions over the web  
(and will be archived for later viewing). You can participate on your  
laptop. Another suggestion I would offer would be for interested  
organizations to arrange a webcast location (requiring only a  
computer, web access and a projector) where local researchers could  
come together to participate in and discuss the conference - we will  
have facilitators to ensure all persons can participate in discussion.  
Some institutions are also holding pre-meetings to discuss the  
project: what it might mean for the campus and how to participate most  
effectively in the Grand Challenge identification process which will  
define the direction of the project. I hope the community will  
consider participating substantively so it will not be left out of the  
conversation, and so it will be positioned to participate prominently  
in the Collaborative as it develops. (Program and pre-registration  
links for both in-person and virtual attendance are at the project's  
web portal.)

To ensure community buy-in and ownership of the Collaborative, an  
independent Board of Directors has been selected which will set  
priorities for the allocation of Collaborative resources to particular  
grand challenges, through a process involving self-forming grand  
challenge teams that will arise from the community and make proposals  
to the Board. The PI's will be available to facilitate the efforts of  
GC teams, but we are agnostic about which grand challenges should be  
prioritized. To ensure substantial independence, the Board of  
Directors was appointed through a bootstrapping process, via a  
Nominating Committee, not by the PI's. One third of the Board will  
refresh annually.

The composition of both the Board of Directors and the Nominating  
Committee can be found at the project's web portal, www.iplantcollaborative.org
. To date, the Board includes biologists Rob Last (chair), Sabeeha  
Merchant, Jim Birchler, Toby Kellogg, Jose Arguello, Susan Singer,  
Russ Monson, David Rand, Jean-Philippe Vielle, and Mark Westoby. An  
equal number of Board members represents the computing research  
community, from bioinformatics to computational biology to computer  
science, information science, and computing infrastructure (Eric  
Mjolsness, Steve Mayo, Fran Berman, Gwen Jacobs, Laurie Kirsch, Mohan  
Tanniru), in order to be able to determine which proposals are really  
tractable and to advise and guide Collaborative management. Thus, the  
Board will possess diverse, balanced expertise with which to evaluate  
any Grand Challenge proposal submitted by the community.

The iPlant Collaborative is funded by NSF's Plant Sciences  
Cyberinfrastructure Collaborative program in the Emerging Frontiers  
division of BIO, as a $50M grant over 5 years to develop a  
cyberinfrastructure for the plant sciences, from molecules, genes, and  
cells to organisms, ecosystems and evolution. As plant biologists, we  
are quite fortunate that our community has been given this unique  
opportunity to lead biology cyberinfrastructure development in the  
service of trying to solve biology’s major, unanswered questions. The  
reason the plant biology community has been entrusted with this  
opportunity and responsibility is, I believe, because we have shown  
exceptional openness, creativity and leadership across disciplines and  
experimental organisms over many years. What better community than  
plant scientists could NSF have chosen for this program? Also, had it  
not been the plant sciences, these funds would presumably have gone  
instead to areas of biology other than plant biology. So, this is an  
extraordinary opportunity for the whole community, and one that we can  
all feel proud to have earned.

Feel free to pass this letter along to your colleagues. I look forward  
to seeing many of you at CSHL, either online or in person, for what I  
believe promises to be a pivotal event for plant biology. We are able  
to waive onsite costs to increase diversity in the conference, so  
please don't hesitate to ask if you feel you are in that category  
(flexibly defined).

More information can be found at www.iplantcollaborative.org,  
including the NSF solicitation, our proposal, site visit questions and  
answers, a ppt presentation, and other documents, as well as 1-2 page  
backgrounders on different aspects of the project. I am available any  
time to discuss the project.

Rich Jorgensen

Director, The iPlant Collaborative

www.iplantcollaborative.org



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