iPG2P Steering Committee
June 14, 2011
Participants
Tom Brutnell | Ed Buckler | Steve Goff | Ruth Grene |
Chris Jordan | Dan Kliebenstein | Eric Lyons | Chris Myers |
Martha Narro | Shiran Pasternak | Dan Stanzione | Josh Stein |
Matt Vaughn | Lin Wang | Doreen Ware | Steve Welch |
Jeff White |
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Agenda
- General Business (5 min.)
- Modeling framework (Steve W, 20 min.)
- Cornell trip (Matt V, 20 min.)
- Demo of TiTo-based tool integration (Matt V, 5 min )
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- Tom is moving to Danforth Center in January.
- Jim Carrington is the new director.
- Danforth wants to have a focus on computational and system biology. Want more grass focus too.
- This presents an opportunity to increase iPlant's iPlant’s interaction with people at the Danforth Center.
- Todd Mockler at Danforth is in contact with Ann Stapleton and Matt V.
- Meetings will be monthly during summer.
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- At end of April, he visited Cornell.
- The visit kicked off a number of interesting initiatives.
- He met with
- Tom's Tom’s group plus C4 people who were visiting
- Ed's Ed’s group Qi
- Chris Myers
- Lucas Muller
- Meeting with Tom
- Tom proposed the Gates C4 community take advantage of some of iPlant 's ‘s infrastructure; possibly a persistent, powerful Atmosphere VM.
- As tools and algorithms developed in such a VM, it should be relatively trivial to push them to DE.
- A more immediate deliverable is an RNA seq pipeline developed by Lin in Tom's Tom’s group.
- Objective is to deploy it in DE at same time the methods paper is published.
- Looks promising to have it available by ASPB as an alternative to Cufflinks.
- Tom will make sure Matt has most recent code.
- Lin wants to submit the paper this week.
- Cufflinks can't can’t deal with strand-specific data sets. Lin's Lin’s scripts can.
- Matt wants to be able to highlight how iPlant enables publication of code coupled with an environment in which it can be used (in contrast to just releasing the code).
- Peak Ranger from one of Lincoln's Lincoln’s group is in DE.
- TB: when code is contributed, is it "required" “required” to be documented?
- MV: We encourage people to document it but can't force them.
- Meeting with Qi (Buckler group and Director of Cornell Bioinformatics)
- Wants to take advantage of iPlant's HPC Foundational API.
- It was in feature freeze, but thawed (added some code), so are a bit behind.
- Meeting with Peter Bradbury and Chi Wazu (?) from Ed's Ed’s group
- They want to push the command line version of Tassel into DE.
- Once Foundational API and DE work well together, we'll we’ll build an interface for it in DE.
- Genome selection, genotyping by sequencing will also be in later this summer.
- Ed wants to teach some classes on genotyping by sequencing.
- Matt is optimistic this can be done in DE this fall.
- Meeting with Chris Myers
- Sloppy Cell – explored if some of it's it’s workflows could be in DE.
- Dependency issue needs to be resolved.
- Meeting with Lucas Muller
- Has been given access to large memory machine with 1 terabyte for tomato and solanace assemblies.
- TB: There is enthusiasm for adopting the iPlant infrastructure. In August Xing Wang will visit. Will things be ready?
- MV: VM's VM’s can be set up any time -- after ASPB.
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- Last week was the TiTo debute of how to build tools in iPlant environment and user acceptance testing.
- Matt live demo'd demo’d how to integrate a tool using TiTo.
- Currently need iPlant support staff to install the app on the cluster. That won't won’t be the case in future. App can be in your environment on the DE.
- About a dozen tools of varying complexity got integrated last week.
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