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You are here: Home Community Minutes Conference Calls 2010 2010-02-16 Tuesday Meeting

2010-02-16 Tuesday Meeting



Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

  1. Matters Arising (<10 mins)
    • Everyone: review the use case list on RoiStorage wiki
    • @For Tuesday, Scott and Josh get a page up with the summary
      • summary - Needs some more review, but largely collated.
  2. Data Storage: Donald's presentation (45 mins)
  3. AOCB (<5 mins)


  • Matters arising (15-15:15)

    • Reviewing ROI use cases, made more clear by the presentation
    • process-summary
      • Review for Thursday? @Yes
      • some are softer requirements; what should happen?
      • avoiding "it's not written I won't do it"
    • bug this morning
      • trying to use OMERO for EM.
      • possibly interesting. already getting feedback.
    • @Jason writes to Agilo for Thursday
    • @Domain registration
    • About pages
  • Data storage presentation (15:15-15:45)

    • intro
      • coming from roi/roi storage mini-group
      • were discussing mechanisms for storing ROIs
      • planned to investigate alternatives
    • "what an roi?" is still a bit open (influences storage)
      • if we want it to be multiple things, then we need to be able to store both
      • Chris: we don't have all of the things defined here (e.g. annotated links)
      • Jason: phrasing? Geometry includes time. Subset of the dimensions.
    • Use Cases
      • user-created/hcs/external/templates
      • "External?" Anything not written by us (maybe scripting as well)
      • different use cases for each type
    • Current storage
      • Pytables doesn't like hetereogenous data, issue with tagging
      • Database linking issues & annotation table size
    • Alternative storage
      • key-value stores require building your own query structure
    • summary
      • mongodb & document db is Donald's favorite
      • bigtables-cousins would be great for purely measurements
      • but we want to do more relational work
    • normalization
      • do we actually use it as a relational db?
      • at the import stage: objective settings, SPW, ...
      • making our life difficult, since we don't make any use of RDB
  • Data storage Q&A (15:45-16:!7)

    • document store
      • use for various things, not just ROIs
      • ROI/ROI-LINKS: doesn't rule it out (not for free)
    • transitional phase is an issue
      • do we want to work toward a single storage mechanism?
      • do we use the best storage mechanism for a particular type?
    • what's the scope? (4.2?)
    • which project would show the utility?
    • Chris:
      • don't currently utilize the ROI object in db correctly
      • InCell you'd tag every ROI with correct tag (cell/nucleus)
      • ROI as an object is un-utilized
    • getting us (and our users) out of a situation.
    • Donald: currently blocked. make this decision rather than later.
  • AOCB

    • @Update estimates by EOF on Wednesday on your work plans
    • @Decide who goes to meetings by Thursday
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