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You are here: Home Community Minutes Conference Calls 2008 2008-10-31 Project Wide Conf Call

2008-10-31 Project Wide Conf Call

Attending: Ilya, Kevin, Curtis, Melissa, Andrew, Chris, Jean-Marie, Brian, Jason, Aleksandra, Donald, Will, Josh


  • Next Data Model release.

  • Other Data Model - Is replicates messing from SPW?

    The query concerns ScreenPlateWell. The experimentalists perform screens using physical plates that were spotted by a robot according to a pre-determined pattern. A batch of each design or layout is made in one go and stored stored in the freezer for later use. The biologist then requests a selection of plates to cover the needs of their experiment, using the replicates to deal with defects and increase statistical accuracy of their measurements.

    So, we have a Screen concept consisting of M different Plate layouts, each Plate layout being replicated N times, so there are M*N physical plates in total (see attached diagram). The issue is how to model the abstract plate layouts (each has a home-made catalogue number) and also the physical plate replicates.

    Currently, as I understand it, there's no abstract concept of a plate layout. Also, to store the replicate number, one would have to let the Plate.Name attribute (or perhaps Plate.Status) contain a compound identifier (eg., Name in 1.1, 1.2, 1.3, ..., 2.1, 2.2, ...), but this obviously nasty as the structure isn't explicit.

    Perhaps, there could be a PlateLayout entity, or similar, that describes the contents of the wells, referenced by Plate. Then Plate would be extended to include {Plate.Name, Plate.Replicate} as a pair of secondary keys.

  • Supporting OME Server

  • OMERO iterations

    • Definition and release schedule for Beta3.2
    • Metadata in Beta3.2
    • Testing OMERO.web
  • ASCB (booth, travel, equipiment, what we want to show)

  • ASCB Poster - improve and update SBS version view here

  • Meeting page instructions


  • Meetings

    • this time on Fridays?
    • Works great (Kevin+Ilya)
    • Be sure to take agenda seriously. Everyone has access to plone.
    • Andrew looking to writing the instructions on meetings.
      • Technology is still a bit unclear.
      • E.g. Skype would be nice if it worked.
      • Curtis & Ilya had it working, Hopefully Dundee next time.
  • Schema

    • release coming up? But does it make sense to hold off.
    • Release as soon as possible? Was a decision made about bindata, tiffdata arity?
      • Change made to model rather than to the code-generation. As Curtis wanted it. Only one or the other.
      • If a third type is added, we can re-evaluate.
    • Ok. Andrew sends out emails this weekend with list of changes.
    • Any other schema questions?
  • Request from Nigel (Heidelberg) re: screens

    • Wants an additional layer between plates and wells
    • His model is strictly hierarchical with plates within screens.
    • Ilya: You certainly have plates in imaging which are replicates
      • But doesn't the model accomadate that with the reagent plates
      • They're disconnected from the imaging plates.
      • Just not a hierarchical structure for just that reason.
      • Chris: Problem may be due to nomenclature. "What's a plate?"
      • Need to come up with a way for representing what Nigel wants.
      • Perhaps small diagrams of various workflows in this model would help.
      • Jason: Similar to Andrew, people are contacting us privately,
        • but all the communication should be pushed toward the user list.
        • Good for the community to see everything that's going on,
        • even if they don't "reply to all"
  • OME server questions

    • Bandwidth on Baltimore's side?
    • Context? Several people have been writing to the list over the last few weeks.
      • Some new installs
      • Some people trying to use OMERO clients against OME-Perl
    • Loci doesn't currently have an OME-Perl server to verify issues.
    • No one is dedicated to OME-Perl other than Ilya. Ad currently out.
    • Idea was to do best effort.
    • New release from HEAD. Backburner project.
      • Database changes, analysis engine, semantic types, internationalization
      • No timeline at the moment.
    • Put WND-CHARM on next agenda? Sure.

    • 3.2 release. Things to fix everywhere.
      • Server: Thumbnails, Sessions, Postgres versions
      • Importer: LSID fixes, file formats, launcher with comment box (codec jar)
      • Insight: problems with textual annotations (with history of moves)
        • Issue with multiple ports for OMEROs on same machine. (Beta4 feature)
      • OmeroJava updated... (inaudible)
      • When?
        • Chris needs time to work on thumbnailing
        • Donald needs to look at some stuff
        • J-M has weird Windows bugs
        • Freeze metadata cycle? And focus starting Monday on release?
        • Merge on Monday? Everything breaks?
        • Jason: Hesitant to break that momentum.
        • Are the bugs critical? Yes. * Leica is most dominant format and it's broken. Etc.
        • Fixing archive original file for Beta3.2? No. * Turn it back on with warning. * Sounds really, really! slow. (Mainly Leica)
        • Need to break all clients to make progress with Metadata
        • Decision: Monday stopping metadata and fixing bugs.
  • Bioformats

    • Try to go to ASCB with 6 of the formats as complete as possible.
    • What's the best way to make this obvious? Have people bring data to ASCB?
      • Visible in ImageJ, OMERO, ...
      • "6 down, 59 to go"
      • Some way to get the point across.
      • Kevin: poster/banner just for bio-formats
        • Agreed. We need these ideas.
        • Melissa + Poster == Good.
      • Corner booth so two open sides.
  • Webclient

    • Testing version and logins available. Will set up a proxy for logins
  • ASCB

    • Andrew is looking into AV materials for hire
    • ...what are we going to demo & what machines/servers do we need to have (running)?
      • How many plugs? Omero server, Plasma monitor machine, 3 laptops at tables (8ft)?
      • In a good location this year.
      • Might make sense to have on loop bioformats opening up files and showing metadata
      • Lots of people didn't have questions for developers, but were just looking.
      • Kevin will bring vinyl banners.
    • Something on outer corner of booth
      • Table with drape? Tall black (display) pillars?
    • Coffee? Costing is unbelievable. 1000USD+
  • Josh loses connectivity...

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