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May 2007 Developers Meeting

2007 Developers Meeting


Location

Meeting will again be hosted by the LOCI group. Location is on campus of University of Wisconsin, Madison. The meeting sites are Room 274 Animal Sciences (at LOCI lab) at 1675 Observatory Drive (on May 3rd) and the Penthouse of Bock Labs at 1525 Linden Drive (on May 4th, 5th and 6th). To get to Bock Labs Penthouse, take elevators up to top floor (eighth) and then make a left and go up stairwell to penthouse. Maps of campus are here: [old-link http://www.civc.wisc.edu/map.html ] campus map, Google map

Dates

Dates are Thursday, May 3rd through Sunday, May 6th. See Agenda for detailed schedule for these days.

Invitees

Dundee, MIT, NIH, LOCI and other OME developers and users.

Travel Info

Most people are staying at the [old-link http://conferencing.uwex.edu/friedrick_lodging.cfm ] Friedrick Center. It is right across the street from Animal Sciences, where the LOCI lab is located. Bock Labs is down the street, at 1525 Linden Drive. Kevin will meet Friedrick Center folks on Thursday morning at 8:30 am.

2007 OME Developer Meeting Schedule


Day 1: Thursday, May 3rd

LOCI conference room, 274 Animal Sciences, 1675 Observatory Drive

TimeTopic
7-8amComplimentary breakfast (will have refreshments at meeting too)
9amKevin-Introduction and logistics overview
9:30amDiscussion of meeting agenda
10amOME Housekeeping and administration
11amUpdate on Grants and review Grant aims
noonlunch break
afternoondiscuss key issues for the future of OME:
1pmOME-XML addition and curation: versioning, OME-XML committee, new fields and constructs (e.g., Prairie), OME-XML compatibility with OMERO
3pmOME-OMERO integration: one system combining the advantages of both


Day 2: Friday, May 4th

Bock Labs penthouse, 1525 Linden Drive

TimeTopic
9amLOCI group presentation
9:30amDundee group presentations
10:30amBaltimore group presentations
11:30amKris-UCSB presentation
noonlunch
afternoonfurther discussion of key issues


Day 3: Saturday, May 5th

Bock Labs penthouse

  • Additional discussion of key issues
  • Implementation plan for solving
  • Identify timeline and delegate responsibilities
    • Goals for the next year
    • Settle on OME grant aims
    • Set milestones for OME-OMERO integration path
    • Release next version of OME-XML before end of May

Day 4: Sunday, May 6th

Bock Labs penthouse

  • Other agenda items and overflow
  • Definition of future plans
  • Travel home

Meeting Notes

Josiah's meeting notes.

OME Madison Meeting May 3-6, 2007



Thursday attendance

Dundee:
Andrew.jpg
Andrew
Brian.jpg
Brian
Chris.jpg
Chris
Jason.jpg
Jason
Madison:
Curtis.jpg
Curtis
Kevin.jpg
Kevin
Melissa.jpg
Melissa
Baltimore:
Ilya.jpg
Ilya
Josiah.jpg
Josiah
Tomasz.jpg
Tomasz

Thursday AM notes: Internal discussion

Thursday PM notes: we discussed bioformats (ask Curtis for details) and walked through changes to the OME-XML standard.

Andrew took notes and posted to the [old-link http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=OME-XML+Evolution] OME-XML Evolution page.



Friday attendance and presentations

Dundee:
Andrew.jpg
Andrew
Brian.jpg
Brian
Chris.jpg
Chris: Presentation
Jason.jpg
Jason: Presentation
Madison:
Curtis.jpg
Curtis: Presentation
Kevin.jpg
Kevin
Melissa.jpg
Melissa

Teresa (AM only)
Baltimore:
Ilya.jpg
Ilya: Presentation
Josiah.jpg
Josiah: Presentation
Tomasz.jpg
Tomasz: Presentation
UCSB:
Kris.jpg
Kris: Presentation

Friday AM presentations: see table above

Friday PM notes: we finished discussing changes to the [old-link http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=OME-XML+Evolution] OME-XML standard.

Andrew took notes.



Saturday attendance

Dundee:
Andrew.jpg
Andrew
Brian.jpg
Brian
Chris.jpg
Chris
Jason.jpg
Jason
Madison:
Curtis.jpg
Curtis
Kevin.jpg
Kevin
Melissa.jpg
Melissa
Eric.jpg
Eric
Baltimore:
Ilya.jpg
Ilya
Josiah.jpg
Josiah
Tomasz.jpg
Tomasz
UCSB:
Kris.jpg
Kris

Saturday AM notes: [old-link Notes/SatAM.Josiah.txt] Josiah's Notes

Saturday PM notes: Discussed differences between OME and OMERO for some time. Primary differences in server-side functionality brought up in discussion were:

  • no support for the STD portion of the OME-XML specification in OMERO
  • access control and data locking explicitly performed on a row-level in OMERO rather than tacitly on a set-of-rows level in OME
  • no support for batch analysis in OMERO
  • no web-interfaced in OMERO

We decided to expand functionality in OMERO then migrate toolsets from OME to OMERO.

  • OMERO will never dynamically upgrade for new semantic types, but facilities will be put into place for importing new STs with a server restart.
  • A new "Event" subclass will be defined that will have set-of-rows access-control and locking.
  • OMERO developers will survey open source workflow environments that could be integrated and have comparable functionality to OME's Analysis Engine. Many bits of functionality managed by the server side Handler classes will be migrated to thin wrappers written in the same language as the algorithm. Major portions of the server API will be migrated to several popular algorithm and "glue" languages. We hope this will allow more direct levels of debugging for algorithm developers, and provide more support for integrating manual and semi-automated analysis tools. Also, we will provide several examples of writing these thin wrappers.
  • A general-purpose web infrastructure will be written by OMERO developers, likely in python using turbo-gears. This infrastructure will use automated code generation to have template-controlled search, display, and object-creation functionality for any defined object-type. OME developers will gradually migrate other functionality from the existing OME web interface.
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