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 mapDates
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 DriveTime | Topic |
7-8am | Complimentary breakfast (will have refreshments at meeting too) |
9am | Kevin-Introduction and logistics overview |
9:30am | Discussion of meeting agenda |
10am | OME Housekeeping and administration |
11am | Update on Grants and review Grant aims |
noon | lunch break |
afternoon | discuss key issues for the future of OME: |
1pm | OME-XML addition and curation: versioning, OME-XML committee, new fields and constructs (e.g., Prairie), OME-XML compatibility with OMERO |
3pm | OME-OMERO integration: one system combining the advantages of both |
Day 2: Friday, May 4th
Bock Labs penthouse, 1525 Linden DriveTime | Topic |
9am | LOCI group presentation |
9:30am | Dundee group presentations |
10:30am | Baltimore group presentations |
11:30am | Kris-UCSB presentation |
noon | lunch |
afternoon | further 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 |
Brian |
Chris |
Jason |
Madison: |
Curtis |
Kevin |
Melissa |
|
Baltimore: |
Ilya |
Josiah |
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 |
Brian |
Chris: Presentation |
Jason: Presentation |
Madison: |
Curtis: Presentation |
Kevin |
Melissa |
Teresa (AM only) |
Baltimore: |
Ilya: Presentation |
Josiah: Presentation |
Tomasz: Presentation |
|
UCSB: |
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 |
Brian |
Chris |
Jason |
Madison: |
Curtis |
Kevin |
Melissa |
Eric |
Baltimore: |
Ilya |
Josiah |
Tomasz |
|
UCSB: |
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.