July 8, 2009
Attendees: Steve, Karla, MMS, Pam, Sheldon, Dan, Michael D.
1. Budget (Karla)
Kate working on a simplified boilerplate template for subcontracts. UA Admin is willing to lower IDC rate to 10%-20%, and possibly the subs can lower their IDC rates as well. The current negotiations are for summer salary only since the post docs haven’t been identified. To get a subcontract, the individual institution needs to send a budget and justification to UA (Karla) and that would begin subcontract negotiation.
2. Trait Evolution (Karla)
Met with Brian Omerara twice. We’ve identified what we need to work on with that group: Independent contrast, continuous, discrete, correlation.
Milestones for Year 1:
1. Identify current limits of software
2. Create DE that accepts trees and data from users and does independent contrasts.
3. To have al the algorithm optimized for 50K tree.
4. To create a 500K sham tree to look at benchmarking standards.
We have a draft project charter and plan. Intellectual scope with be wider than independent contrast.
AI: Check charter to make sure that there is intellectual breadth.
?? Will Brian scale algorithms for a single character mapping on tree?
?? Could that group include geographical reconstruction?
Sheldon and Karla will check with Brian and bring this to next working group.
3. Tree Reconciliation (Sheldon)
Todd was a guest speaker last week. He was able to communicate at different levels: Background to developers, organization perspective,.
Next steps: we need to get clarification on the actual lead (Todd or Danny Durand), and we have been working on draft of the charter and project plan.
AI: Provide list of team members.
4. Data Integration (Sheldon)
Group is headed by Val Tannen and Bill Piel. We are following up with looking for some more detailed guidance. We are coming up with questions that are cross cutting to bring to Val since this is such a cross cutting topic. Taxonomic intelligence (taxon ID mapping): we are contemplating this as an adjunct to this group. This is an important area but EoL is working on it. There is a tree visualization proposal that looks likely to get funding.
5. Data Assembly (Karla)
Looking at the best place to host this and the number of participants involved, NSF confirmed that they would like to get synergy from iPlant via Letters of Collaboration. NSF would like iPlant to support new proposals that take advantage of iPlant activities. It would be good to set a cap for participants and consider diversity for the Data Assembly meeting. 50 people including iPlant dozen, have an A list and a B list. Possible location is Phoenix.
AI: Pam and Michael D. will send participant list to Sheldon and Karla this week.
6. Big Trees (Dan)
Sheldon has spoken with Alexis and his is working the people at ASU to use the 60 K taxon tree (based on 8 genes). His estimate is three weeks of clock time to run that analysis. They fall into the core expertise for the HPC people and TACC people.
7. APWeb2 (Sheldon)
This is a more dynamic representation of data. This was started by and maintained by Peter Stephens (U of Missouri). It tries to cover phylogenetic relationships for groups of angiosperms and beyond. It is fairly flat. It is not easy to search and not laid out consistently. Lots of people in plant diversity use it as well as educators and those who what to look up anything about a plant group. It would be highly valuable if we could make it more accessible and searchable. Cam Webb and Amy S. were working doing this. As an education project of iPToL, it can be done quickly, with a concrete product, and the public at large would appreciate it. If we really wanted to think about outreach to lower grade levels, then APWeb2 is too complicated. But it would provide background transferable to other/younger age groups. This is a great teaching tool to undergrad and grad students. This FTE estimate is low, could take as much as a full-time developer, plus a graduate student for data curation. We need more iteration before we can have a full opinion. It is possible to put a GUI on the current product., but won’t be able to move on this until the fall (Amy and Cam are not very accessible this summer). iPlant needs a list of requirements of that we need to satisfy.
Mike Sanderson sent a draft of the ad for Nature/Science. It would be good to have a link to iPToL information (web presence needed to show scope of whole project). Ads need to point to clear job openings.
AI: Karla needs feedback in track changes mode.
AI: Mike will write up executive summary for iPToL project for website.
AI: Webpage needs to be up when ad gets released.
AI: Is iPlant getting what it needs out of the steering committee?