iPlant collaborative main page
What is a "discovery environment"? (PDF)
Assembling the Tree of Life for the Plant Sciences (iPTOL): summary (PDF), proposal (PDF), intro conference (agenda), more videos
Intro presentation (PDF, 4.6 MB) by O'Meara to iPlant engagement team (June 17, 2009) [note: I should have mentioned phylocom and the CIPRES portal as existing tools, too].
Our working group (so far)
By Karla Gendler, iPlant Project Manager, gendlerk@iplantcollaborative.org
iPlant officially kicked-off the Phylogenetics Grand Challenge project, meeting with the seven iPlant Tree of Life team leads at NESCent in Durham, NC, on May 7-8, 2009. The threefold goals of the meeting were ambitious: 1) define the collaborative relationship between iPlant and the Principal Investigators of the iPlant Tree of Life (iPToL) team; 2) develop a management plan for the collaboration project; and 3) create a roadmap for work to be carried out over the next two years.
To achieve the project goals in the 2-year timeframe, four collaborative working groups were proposed, each having focused development goals. Comprising each group will be an iPToL superuser or faculty member designated as the lead and point of contact, post-docs and/or graduate students, and members of iPlant staff assigned to the Grand Challenge project. The four main groups are: 1) Big Trees, focusing on construction of large phylogenetic trees greater than 50,000 species; 2) Data Assembly, focusing on assembling the data to produce large trees; 3) Tree Reconciliation; and 4) Ancestral Character State Reconstruction. Additionally, two crosscutting working groups, Data Integration and Visualization, were proposed to develop shared data and compute infrastructure. Working groups will self-organize and meet, via phone, as required. While actual implementation of the four main working groups will be somewhat staggered, organization of all working groups will commence as soon as possible.
To oversee the progress of the working groups and manage overall project coordination, a Steering Committee comprising Michael Sanderson, Michael Donoghue, Pam Soltis, Dan Stanzione, Steve Goff, Sheldon McKay, and Karla Gendler will meet monthly.
The kickoff meeting also tackled the very important issue of compensation. Although the budget for the Phylogenetics Grand Challenge is still under consideration, compensation methods for community members involved in the project will include a competitive fellowship program for post-docs and graduate students, along with summer salary support for faculty. Support for workshops, meetings, and travel will also be included.
The team also proposed two workshops over the next two years. The first workshop, to be held late fall/early winter 2009, will be on Data Assembly. This workshop will bring scientists together to begin to identify the gaps in current data so that new data could be generated, on separate funding, when tools are ready to run a new large tree. The second workshop, proposed for 2010 in Europe, would present an opportunity to engage a broader set of international collaborators.
In summing up the kickoff, iPToL team member Michael J. Sanderson said, "we had to re-formulate and re-focus in some novel ways, but we are pretty confident that these activities will lead to something exciting."