SC_20100727

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Last updated: Jul 29, 2010Version comment
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iPG2P Steering Committee
July 27, 2010; 2 to 3 pm EDT

Present: Matt Vaughn, Doreen Ware, Karla Gendler, Steve Goff, Chris Myers, Dan Kliebenstein, Dan Stanzione, Tom Brutnell, Steve Welch, Greg Abram, Jeff White, Ruth Grene

Notes/Agenda:
CI Development Update - Vaughn, Gendler, Stanzione

  • Discovery Environment, after 3 weeks of post-deployment testing, debugging, feature modification, had been released (version 0.2)
    • Steering Committees of both GCs and working groups
    • seems to be stable and delivers scientific objectives (PIC and three sequencing related workflows)
    • demonstrates revised UI and backend has been made more robust and scalable;
  • Prototype application for Visual Analytics group
    • Greg Abram, Lecong Zhou, Karla Vega, and Matt Vaughn are working on proof of concept of ideas that have emerged from VA meetings and discussions
    • demonstrate that you can chain various scientific tools together to deliver relatively interesting science
    • Vaughn demonstrated in Twiddla
      • take data set of genes and contrasts
      • for coloring in table, colored according to p-values
      • can select one or more of contrasts by clicking on boxes, creates union and submits to genemania or aranet
      • results pumped into window that has cytoscape running in it;
      • Feature request: want a link to eFP browser but not by August 10 deadline
    • just a prototype
      • at service layer there is a parameter that supports species but integration requirements for all species have not been met
    • should be completely modular and only have one interface that you have to learn
    • this particular workflow is being put out as a working prototype and is going to be hard-wired together
    • long term plan is visual programming environment will eventually subsume this
    • will start to move in to DE to make this workflow work and then other components also;
  • BrachyBio
    • make use of Tom’s brachy project for EOT and be based on my-plant social networking site
    • My-Plant is scheduled to be released later this week which bodes well for integration with BrachyBio;
    • work has been completed on the module development but needs development feedback and iterations
    • This summer:
      • about 8 teachers that are bringing about 1000 EMS lines to classroom
      • has talked about my-plant and modules
      • translates to about 300 students doing phenotype screens
      • mutant frequency is about 20% with very obvious phenotypes and lots of cool looking mutants
  • status of GLM
    • Ali and Dave were having success implementing core of GLM on GPU, have not moved code to TACC but have proof of concept
    • traditional C-implementation
      • skipped straight to parallel version, full up MPI version and built on PetC
        • made implementation more complicated but skipping step of sequential C-program; will be full implementation
  • encourage you to use DE, need additional user feedback on how well it works, how fast it goes; few things we know we need to fix but if other things that are needed, please file support ticket and/or let us know.

Feedback on DE release - All

  • Test files have been provided and a description can be found in the user manual
  • Others do not see your folders yet, only you
  • Still have security certificate problem, Gendler will ask for purchase of signed certificate
  • Need for better error handling and file handling
    • one change we will be implementing is to ask what type of file it is that you are importing/uploading
  • Tools being used can be found on the landing page and in the user manual
    • In future, a report will be generated that shows all tools and commands run
  • Will need a few meetings to discuss tweaks and features to identify priorities
  • API will be talked about at ASPB but Developer Took Kit will be out in September so can start to integrate tools

Next meeting time:

Adjournment: