iPg2p Steering Committee Minutes
November 4, 2009; 1 to 2 pm CST
Present: Steve Welch, Karla Gendler, Steve Goff, Ruth Grene, Tom Brutnell, Chris Myers, Jeff White, Dan Kliebenstein, Chris Jordan, Dan Stanzione
The meeting was convened at 1pm CST and there was some general discussion to allow time for late arrivals to dial in.
Item 1: Review Action Items
- All: rewrite postdoc ads to be more specific in the needs of the working group. Once received, they will be reposted at the sites the old ads have been posted at
- Grene began to rewrite her ad but then had a fantastic candidate apply so this is put on hold
- Welch will contact the headhunter and gain access to the database and see if it is worth while
- Has not had time
- All: send Welch contact information of your institutions media relations offices so he can coordinate the press release
- Welch reported that he still needs contact info from UA, CSHL, Cornell for Myers. Welch will check with Buckler to see if he should go with ARS. The press release will have common text but then will be given to the local press offices to write/rewrite with a local slant to highlight those working at the respective universities. Welch will write the first draft of common information.
- Gendler will set up anonymous doodle poll for voting on uses cases
- White brought up an outstanding action item regarding in-house training. He will circulate what he has received and post a reminder to people to add in more information. Goff suggested that Dave Micklos be included on emails regarding training.
Item 2: Use Case Poll Results
10 - Carbon metabolism (inc. C3 & C4) and flowering time
8 - Hypothesis- Generation through Data- Mining, Processing, and Visualization
6 - Lignin biosynthesis
3 - Screening Brachypodium phenotypes in high school science classes
2 - Floral phenology in less studied species
Welch reported that there appears to be three categories of use cases. With the lignin group, the have the data but might logically be the group to test out modeling tools. Goff commented that the lignin people were surprised that we had a modeling group and are very interested in being involved with iPlant. He said that there are two engineers that are scheduled to come in and help but that he does not know who they are, what their backgrounds are, when they start, or how to interact with iPlant. Myers suggested that perhaps the engineers could join the modeling group. White said it would be best if the modeling group met first to discuss this possibility and also the background of the lignin project. Goff has agreed to arrange a conference call with the lignin people and with White, Myers, and the rest of the modeling group.
In regards to Brachypodium, it will be necessary to assess the budget relative to the priority that has been voted on. Brutnell added that this is strictly an EOT activity and that maybe the group should think about other EOT activities that tie directly in to the primary biological use cases. Goff said that EOT is starting ot coordinate with the Grand Challenge teams and it is important that Dave Micklos be brought in so that he can weigh in on the subject. Also, Sue Wessler is interested in running a national scope EOT activity in conjunction with iPlant. Brutnell has agreed to circulate to EOT a one page executive summary with budget.
Welch and White had the opportunity to discuss floral phenology and decided that it would be best if they could look for data sets that have phenolgy (such as solar metaboloism) to serve as an ancillary project to carbon metabolism. Brutnell added that the biggest data sets will deal with flowering time.
Welch said that iPG2P should focus on the first 2 use cases that are at the top of the list. Grene agreed. Welch suggested that he, Grene and Brutnell get together Friday night at the Visual Analytics meeting to discuss interrelations between the use cases. Welch will be presenting on modeling and viz needs and will raise some of Kliebensteins points regarding eQTL.
Item 3: Data Integration Priorities
The Data Integration working group has put together a questionnaire to sed out ot large data providers and has asked for input. Welch asked as the information comes in, what should the DI group attact next? Jordan added that the group decided to focus on the NGS pipeline, looking at data formats for genomic sequence and annotations and also exchange standards. Grene commented that she was disappointed that the group was only focused on NGS and that in her presentation on Friday, she will make her needs known. Brutnell said that there has been a discussion within the NGS group as to what data needs to be tracked through the pipeline and can be found in Vaughn's document. Welch added that the StatInf group is making strides in format requirements and how can NGS work with that? It appears that a tabular format with appropriate meta-data is emerging as what is needed. For StatInf, the group is talking about the metadata that needs to be supplied for statistics and also for modeling. It was decided that the next priority for the DI group is to start receiving meta-data descriptions from the groups and to being to deal with the questions of how to organize this metadata and also to think about what is going to be the minimum amount of information for any data in iPlant. Jordan said that this is linked to provenance and that we should be well prepared for that. White suggested that instead of using "data type" we use "data domains".
After looking at the questionnaire, Grene said that Soybase and Gramene are missing from the list of providers. Goff commented that NSF is using TAIR as an example of not funding non-innovative databases and that TAIR's process has to be propagated. Welch stated that databases need to be in machine readable form and that we are now in a position to start to prioritize datasets/databases and we need to consider practicalities. Jordan said it is necessary to define the socpe of the problem but we first need to identify as broad a set of data providers as possible and then prioritize. Myers added that the vize needs need to be pushed down to DI. White will be at the Summit and can start talking with Gates Breeding and iPlant and that it would be good to go over the questionnaire with Graham McLarren. All should provide a list of data providers to Jordan.
Item 4: Identify Action Items
- White post in-house training material that he has collected and solicit comments/additions
- Gendler provide UA and CSHL press contact information to Welch
- Welch to check with Buckler about his press contact information
- Welch to draft the common text for the press release
- Goff to arrange a conference call between modeling group (White, Myers) and lignin group
- All provide feedback about data providers to Jordan, either on wiki or in email
- Gendler to query modeling group about setting up a modeling telecon
Next meeting time: Wednesday, November 11, 2009, 1pm CST
Adjournment: The meeting ended at 2pm CST