2010-05-11 Tuesday Meeting
Attending: Brian, Ola, Will, Jean-Marie, Christoph, Ingvar, Andrew, Jason, Josh, Melissa, Carlos - Has ASCB Timetable
Agenda
Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)
Accepting minutes from last meeting
Matters Arising (<10 mins)
- Everyone: Review tickets, any new functionality in backlog
- Andrew: Reply about find spots (something about cellprofiler?)
- Andrew: Put up an ASCB times table
Visiting EBI Speaker's Ingvar Lagerstedt & Christoph Best presentation (45 mins)
ASCB Timetable
Key deadlines - Full list available here
Deadlines June 4 - Application to qualify for booth assignment according to priority point system - 50% of booth fee mailed with application - Exhibitor Showcase application and deposit - Tutorial Program application July 29 - Regular Abstract Submission (talk or poster) Aug. 13 - Balance of booth fee due - Deadline for 50-word product description to be included in the ASCB Annual Meeting Program Sept. 1 - Regular Abstract Submission (poster only) Sept. 17 - Exhibitor Service Kit (carpets/power/furniture) Oct. 1 - Hotel: Booking Deadline Oct. 2 - Hotel: Final rooming lists Oct. 7 - Attendee Early Registration (for discount) Oct. 14 - Late Abstract Submission Dec. 1 - Hotel: Changes/Cancellations Dec. 9 - Setup 1:00 pm, to 5:00 pm Dec. 10 - Setup 8:00 am, to 5:00 pm Dec. 11 - Setup 8:00 am, to 12:00 Noon Dec. 12 to 14 - Exhibit Hall 10:00 am to 4:30 pm Dec. 14 - Dismantling 4:30 pm to 9:00 pm Dec. 15 - Dismantling 7:00 am–12:00 Noon
AOCB (<5 mins)
Notes
Last Meetings' Minutes approved
Matters arising
- Brian still working on testing script (right after importer updates!)
-
Andrew responding to FindSpots
- Writing to Ilya for a response?
- Possible we'll get more detailed questions (segmentation, etc.)
- ASCB page is up with timetable
EBI presentation
- PDB, 65,000+ entries
- EMDB curated database, paid to review the entries
- doing segmenation 'by hand' using Amera or Imod
- some entries are embargoed (up to 2 years)
- simple (old, 2001) data entry form
- goal (2012) of join EMDB and PDB
- currently 'encouraging' people to enter both with cross-links
- most important feature of atlas is downloading the maps and viewing locally
- trying to do more dataharvesting by integrating with eman and other management system
- appaling lack of image standards makes it a challege
- currently only storing final results. more interesting now to store everything
- Q: eman2 offers HDF5 A: but no agreement on what will be stored
- looking to formalize a system using Ontologies
- rich data: 40 classes, 64 pdb files, ... and where they should be display
EBI discussion
-
Q: health/status? community interaction, ...
- community is usually quite positive
- but the number of entries is going down
-
problems: metadata management (don't have the interesting metadata)
- and difficulty in expressing the tomograms
- currently neither the technology to record or display
- stuck with one map per entry (more are variations of experiment)
- Ingvar is working on displaying segmentations (color markups)
-
Q: health/status? community interaction, ...
Ingvar demo of astexMoleculeViewer
- 2 ways of visualizing segmentation
- trying to fit your already known structure into the EM map
- their format is based on the original mapman format with some header changes
- needs some optimizations
- java based - can be a rendering bean for web use
- can match up pdb maps 'by hand' to build larger molecule structures (like chimera)
- can combine atom coordinate data with pdb maps
- working on importing other formats (ex. seger). Not perfect yet!
Actions
- Everyone think about annotations for Thursday discussion (see nitpick thread)