[Arabidopsis] The iPlant Collaborative: what potential does offer for Arabidopsis research?

[Rich Jorgensen]

Dear Arabidopsis  colleagues,

I'm writing to encourage you and your colleagues invest a little time  
in understanding the iPlant Collaborative and thinking about what it  
might do for the plant sciences. Background 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 would also suggest that you 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 www.iplantcollaborative.org 
). Participation in the conference is NOT necessary for participation  
in the Collaborative, but may be helpful in understanding how best to  
participate.

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, preferably through Grand Challenges integrated across  
levels, 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 "if we build it, they will come."  
Rather, the community must first come together and decide WHAT we  
should build! Until that happens, no cyberinfrastructure will 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 the field, 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 to discussion of what these GC's should  
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.)

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. So, rather than "build it and they will come" the  
approach of iPC is to get to the community to come and then build what  
they actually want rather than what we think they might want. 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, allowing new  
members of the community to serve.

The composition of both the Board of Directors and the Nominating  
Committee can be found at the project's web portal, www.iplantcollaborative.org 
. The inaugural Board includes biologists Rob Last (chair), Sabeeha  
Merchant, Jim Birchler, Toby Kellogg, Susan Singer, Russ Monson, David  
Rand, Jean-Philippe Vielle and several others to be recruited, mainly  
in the EEOB area and internationally so that field will be well  
represented. An equal number of Board members represents the computing  
research community, from bioinformatics to computational biology to  
computer science, information science, and computing infrastructure,  
in order to be able to determine which proposals are really tractable  
and to guide Collaborative staff in designing the right CI. Thus, the  
Board will possess diverse, balanced expertise with which to evaluate  
any Grand Challenge proposal submitted by the community.

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 understanding which are the most compelling and  
tractable grand challenges in the plant sciences that will 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  
campuses to arrange a common webcast location (requiring only a  
computer, web access and a projector) where campus 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 Arabidopsis 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.)

The iPlant Collaborative is funded by NSF's Plant Sciences  
Cyberinfrastructure Collaborative program as a $50M grant over 5 years  
to develop a cyberinfrastructure for the plant sciences, from  
molecules and cells to organisms, ecosystems and evolution. As plant  
biologists, we are all fortunate to have this opportunity to lead  
biology cyberinfrastructure development. The plant biology community  
has been entrusted with the opportunity and responsibility because, I  
believe, we as a field have shown exceptional openness, creativity and  
leadership across disciplines and experimental organisms. What better  
community than plant scientists could NSF chosen for this program?  
Also, had it not been the plant sciences, these funds would presumably  
have gone instead to other areas of biology, not to plant biology. So,  
this is an extraordinary opportunity for all plant scientist, and one  
that we can all feel proud to have obtained.

Feel free to pass this information along to your colleagues. I look  
forward to seeing you at CSHL, either online or in person, for what I  
believe promises to be a pivotal event for plant biology. I am 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).

I am available any time to discuss any aspect of the project.

Best regards to all,

Rich Jorgensen


Richard A. Jorgensen
Plant Sciences & BIO5 , University of Arizona
Director, The iPlant Collaborative
www.iplantcollaborative.org