2010-08-24 Tuesday Meeting
Attending:
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)
- 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)
Will & Ingvar will be presenting latest on EMDB
N-Dim & SPIM Update
AOCB (<5 mins)
Notes
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
EMDB Demo
- @mage/webemdb/publications/ for a demo view of the work
- EMDB Presentations page shows a good number of publications added
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'Show All' will display all the entries available
- Gets XML and Gifs from project for presendation
- Can view XML directly if desired
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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
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EMAN2 example entry: @mage/webemdb/entry/1080/
- Shows particles and raw data
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Allows filtering and script processing
- fft, merdian, median2, and log filters
- nonlinear anisotropic diffusion & movie ROI scripts
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Discussion:
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Jean-Marie: Why use this over their existing tools?
- Richer presentations, collaborative features, online analysis
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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
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Jean-Marie: Why use this over their existing tools?
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Christoph's Presentation
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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
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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
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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
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Discussed how they handle the XML definiation and use of RDF data
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Concrete plan:
- Jean-Marie: Should use the existing EMDB schema as a starting point
Other points
- Will carry on for SPIM converstaion on Thursday