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You are here: Home Community Minutes Conference Calls 2010 2010-08-24 Tuesday Meeting

2010-08-24 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. Accepting minutes from last meeting

  2. Matters Arising (<10 mins)

    • Review minutes from Tuesday/Gianluigi for Tuesday since they were posted late
    • Will: Review tickets#2603 and #2606. If they are large, move to stories
    • Andrew: add ticket on SPIM
    • Jason: Talk to Curtis about the ImageJ conference (can he add a few words about us)
  3. Will & Ingvar will be presenting latest on EMDB

  4. N-Dim & SPIM Update

  5. AOCB (<5 mins)


  1. Accepting Last Week's Minutes: Accepted

    • Ongoing conversation with Gianluigi
    • @Jason will get the presentation for the website
    • SPIM story was created
    • @Jason still needs to talk to Curtis about ImageJ
  2. EMDB Demo

    • @mage/webemdb/publications/ for a demo view of the work
    • EMDB Presentations page shows a good number of publications added
    • 'Show All' will display all the entries available
      • Gets XML and Gifs from project for presendation
      • Can view XML directly if desired
      • IMod visualization shows various ways to view the data
        • OMERO viewer shows MRC image
        • Additional annoations viewable
        • Offers a resized map for web-browser viewing
        • Where available, offers PDB protien data
        • Still needs some controls to allow optional viewing modes
    • EMAN2 example entry: @mage/webemdb/entry/1080/
      • Shows particles and raw data
      • Allows filtering and script processing
        • fft, merdian, median2, and log filters
        • nonlinear anisotropic diffusion & movie ROI scripts
    • Discussion:
      • Jean-Marie: Why use this over their existing tools?
        • Richer presentations, collaborative features, online analysis
      • Donald: is it possible to unify the "publication" efforts
        • Three currently: JCB, ASCB, EMDB
        • They all have a central list of entities
        • Nice to have a common presentation/representation between parties
        • cF. AlternativeStorage and RDF
    • Christoph's Presentation
      • Discussed how they handle the XML definiation and use of RDF data
        • Their properties are easier to use then standard XML represenations
        • Easier to add metadata, making it very extensible
        • These additional attributes are very useful for Tomogram data
      • ImageStacks and naming
        • How do we deal with stacks of images?
        • Each image in a stack needs some sort of unique URL for naming
      • Useful relationships to expose would be:
      • Image appears in the same coordinate frame
      • Images related by process steps
      • Will: Would be nice to have a processing/image chain
      • Chris: Need a balance between flexibility and understanding of data types
        • Donald: Would be good to find what is coming between publishing requirements
        • Jason: This would also have scientific benefit
    • Concrete plan:
      • Jean-Marie: Should use the existing EMDB schema as a starting point
  3. Other points

    • Will carry on for SPIM converstaion on Thursday
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