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iPg2p Steering Committee Minutes
September 22, 2009; 2 to 3 pm CDT

Present: : T. Brutnell,, K. Gendler, S. Goff, R. Grene, D. Stanzione, M. Vaughn, S. Welch, J. White, C. Myers, MM Sprinkle, D Kliebenstein

The meeting was convened at 2pm CDT and there was some general discussion to allow time for late arrivals to dial in.

Item 1: Review Action Items

  • White/Myers: Generate a mutual education proposal

White reported that there are 4 categories of education: 1) individual mentoring/instruction, 2) self-guided study (directing to key references and videos, ShowMeDo), 3) workshops, and 4) short courses of 1-2 weeks in length with costs > $1k (should be mission critical if sending someone to course).  Key question is what will be available from iPlant in terms of web resources (external vs internal, with internal being who to ask regarding a specific topic).  The subject-centric view (wikis, etc) might work better for this.  Myers thought it might be best if education is more organic with people identifying their own needs.  This will require that the right type of web based environment be set up to encourage collaboration.  Perhaps WebEx should be used.  Also, can look at mutual education as being personal versus subject centric.  If having more organized meetings is desired, then the subject matter should be identified.  White commented that there are two types of training: self-directed and hand on training (or training to bring up to speed and then training to learn how to use tools).  White agreed to compile list of resources (books, references, tools) from everyone and requested that with references, it would be nice to explain why the reference is good.

  • Gendler/MMS: Start planning for project meeting late January

Gendler reported that a time and a place is needed so logistics can be worked out. Idea was to maybe extend PAG but this would conflict with the iPlant BoD meeting and also with other satellite meetings. Gendler will set up a doodle poll to find time for first 3 weeks in January.

  • Goff: Follow up with Susan and/or Michael Norteck to get more details on grant opportunity

Goff reported that Susan Greigorich would very much like to coordinate with KnowledgeBase funding and suggested that iPlant sit on board for reviews but Goff pointed out that this could be a potential CoI. Both NSF and DOE support the coordination efforts with iPlant. Goff thinks that the call is for computation proposals and has agreed to send proposal to all working group leads. Brutnell will contact Greigorich about web lab experiments/data taking.

  • Welch: Circulate ppt for further input from iPG2P

Gendler will circulate and will post on Confluence site.

Item 2: Working group reports (5 minutes each)

  • Visual Analytics (Ruth)

Grene has posted 3 documents to the Alfresco site; one is formulation of problem statement based on discussions with Ware and the other two are slides. The group met last week and Grene spent time explaining some of the plant biology behind the slides and also showing flow chart of what is needed when asking "what is the function of my gene of interest?". The goal of the group is to view data that has been integrated.

Grene commented that there is a need to bring CS up to speed on nature of data and that going back and forth with emails and teleconferences will not suffice. Stanzione suggested maybe a small get together of the working group. Welch asked if there would be a way to capture this interaction for others to view later. Brutnell suggested that this is larger than the working group and maybe there is a need to get more people together but Stanzione suggested only planning around a few key people and inviting others so it doesn't take so long to plan.

  • Data Integration (Doreen)

Deferred until next week.

  • NGS (Tom)

This working group is trying to create a public interface to help with DNA and RNA sequencing. The group has split into two subgroups with DNA-seq/SNP being led by Ed Bucker and RNA-seq led by Brutnell, Bob Schmitz, and Todd Mockler. The RNA group has created a work flow that takes data from sequencing centers, runs through different algorithms, and outputs can represent gene count/gene expression. They have decided to modify RPKM, the standard used in humans. Mockler has done a lot on tool development and has developed an assembler TAP.

Other side to this is also annotating the trascriptome. Mockler was written some code to do this but the modules don't talk to each other so this might be worth looking into. Schmitz uses SOLID technology, which is gaining momentum, but the tools for Illumina don't work with SOLID and thus presents another opportunity for further development.

Work flows have been uploaded to Alfresco and the working group has the chance to read and comment on them and then the group will present to Matt for requirements gathering.

  • Modeling (Chris M)

Myers reported that the group is getting hung up on use cases and finding the uber use case. Perhaps it would be better to integrate results from other working groups. Myers asked if there are common use cases and Welch suggested coupling photosynthesis modeling with flowering time. Myers posed a lot of questions and stated that there is a need for sufficient metadata for models to work. Part of what Myers does is a lot of screen scraping and would like scripts to do this (data integration problem). Myers will survey modeling group to find common tools and common hangups that then can be addresses so the group can proceed.

Item 3: Developers Meeting Update (5-10 minutes, Matt V, Steve W)

Vaughn reported that Developers Meeting had two purposes: 1) a chance to meet and get to know everyone in person and 2) setting how the development group will work together. From an Engagement Team perspective, it was good to understand the types of questions that the developers will need to have answered for requirements gathering. Welch added that the method of operation is understood in that the group is trying to build a model of the user so that they know what they are up against when/while the software is being built.

Item 4: Marquee Biological Scenario (Matt V)

Vaughn raised the idea of having biological questions that are cross-cutting that would lead to progress. These questions would be developed as the working groups are moving forward now but it is important for us to find some biological question to start at and walk through the analytic framework that is used or needed to solve the question and ask why can't we do this now. We need to ask ourselves what are the gaps/limitations and then use these for product identification. It will give us a framework for cross-cutting issues. It also would be a way to avoid developing a set of tools that are not connected.

Welch suggests that on the trip that he and Goff will be taking, this issue be addressed and it will be their mission to flesh out the details of the biological use cases.

Item 5: Assign Action Items

  • All: Send Jeff White list of references/resources/topics for mutual education, including a sentence or two as to why the reference is good
  • White: Compile list of references
  • Gendler: Circulate Doodle poll for first three weeks in January for project update meeting
  • Goff: Circulate RFP
  • Brutnell: Contact Greigorich regarding web lab experiments
  • Gendler: post Welch's presentation given at developers meeting

Next meeting time: Tuesday, September 29, 2009 at 2pm CDT.

Adjournment: The meeting adjourned at 3:22pm CDT.