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Conversation with CAMERA - with Guillome, Dongying, Tom, Jonathan and from CAMERA Ilkay

Original email from CAMERA

Hi Jonathan,

Madhu and I were just discussing how we can revive the STAP workflow in CAMERA and had some questions.

Would you have any time this Thursday? Any time between 11am and 3pm is good for us.

Thank you! -ilkay

-- Ilkay ALTINTAS Deputy Coordinator for Research, San Diego Supercomputer Center (SDSC) Lab Director, Scientific Workflow Automation Technologies (SWAT @ SDSC)

University of California, San Diego 9500 Gilman Drive, MC: 0505 La Jolla, CA 92093-0505 Phone: (858) 210-5877 Fax: (858) 534-8303 Web: Skype: ilkay.altintas


  • May 5, 2010 - 3:20 PM - 3:50 PM
  • Involved from CAMERA: Ilkay Altintas <> madhu <>, Shulei Sun <>,
  • They started conversaiton by saying they are working on STAP and had some questions
  • Eisen asked them to back up and have general discussion of plan
  • CAMERA has a version of STAP they are ready to share
  • CAMERA asked how one can use STAP to do OTU clustering and trees of metagenomic data
    • Eisen tolkd them that this was not within STAP really and STAP was focused on taxonomic naming of sequences
    • We agreed that a good output for STAP in CAMERA would be graphs and charts of relative freqeuncies of different taxonomic groups
    • EIsen mentioned WATERs and sent submitted paper on WATERS to CAMERA people
    • We discussed how WATERs uses the COMAD version of Kepler which CAMERA does not use
    • Ilkay will look into it but suggested it will be easier to work with their version of STAP not the version in WATERs
  • Phylogeny and OTUs
    • Then we discussed phylogeny and OTU issues
    • They are interested in making Kepler workflows for Tom and Kembels tools
    • Tom will send them code so they can start to think about how to implement it
    • Tom said code is not fully finished but happy to share
  • CAMERA told us they do releases every two months or so and could release STAP in one of these interim releases of CAMERA
    • CAMERA noted they have an XML implementation of visualization tools
    • When they build workflow - can pipe into visualization tools
  • CAMERA will send bundle with STAP workflow
    • We will check it out
    • Plan for phone call in two weeks