[Gramene-announce] Announcement for iPlant Collaborative

[Chengzhi Liang]

Dear Plant Researchers,

An iPlant Collaborative program has been initiated. You can go to 
Gramene website (www.gramene.org) for a detailed description.

I also attached the text below.

Regards,
The Gramene Database.

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

I'm writing to encourage creative thinkers in the plant biology 
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 that "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 <http://www.iplantcollaborative.org/>