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November 2006 Developers Meeting

Nov 2006 Dundee Meeting Topics


This meeting is simply a chance to catch the collective OMERO/Shoola breathes as we near the completion of M3 for both OMERO3 and Shoola3. M3 has included a significant addition of functionality on both server and client. In addition, we have used it to forge an alliance with [old link href="http://www.usableimage.org" UsableImage]. All sides agree that this has been a very powerful exercise.

Various informal discussions have agreed that M4 will involve a relatively small jump in functionality, focussing on usability and deployment. M4 will then serve as the basis for RC1, done hopefully by end of 2006.

At this meeting, we will:
  • tag OMERO and Shoola M3
  • define M4, and thus RC1
  • Ensure all tasks are ticketed and assigned
  • define future interactions between OMERO, Shoola, and UsableImage.
  • Begin defining our next major steps (post release of OMERO3/Shoola3).


Draft Programme (please make comments etc as necessary)

TimeTopicLead(s)Comments
09:00Coffee, setup, gossip
09:45Summary of StatusJason, Catriona
10:00Defining M4 and RC1Chris, Jean-Marie, BrianInstall, User Admin, Deletes, Docs
11:00Defining Future Features and ProcessAllSee below for Features How do we use the UI/OMERO process to design this functionality??
15:30Tickets on trac, Notes on Tiki, Docs on UsableImage
17:30Wrap up



Some suggested Features (comments please!!!!)

  • Scripting & Workflows
  • Events
  • Indexing
  • Lab Notebook
  • HiBrowser
  • AdminTool
  • Flexible annotations
    • Allows .txt/.html/.xml/.pdf/.doc/... to be attached to nearly anything
    • in combination with Lab Notebook
    • similar model needed
  • Provenance (History/Versioning/Audits)
  • Validation
    • Not a user visible change, but one that directly affects all users. Currently a significant percentage (20-30%) of the model UML is NOT implemented in the server. These are constraints that don't take place at the SQL level and need code. This code possibly go hand-in-hand with Josiah's idea of various spec-levels. (Josh)
  • Working Sets
  • ROIs
  • User feedback and bug tracking tool
  • Installers
  • User Admin System
  • One idea
    • we need scoping exercises for each of these
    • what is required, what dependencies are there, what changes to data model etc. Process? Finally, we need some time, roughly a month, for local deployment, consortium building, and paper writing. What about first 4-5 weeks of 2007?


Dundee Meeting 2006-11-16


In Attendance:

Brian, Jason, Catriona, Donald, Chris, Jean-Marie, Paula, David

Opening Statement from Jason:

  • May need to change scope of the meeting to concentrate on what's in RC1
  • RC1 should be ready for December 15th
  • Today we need to work out a way to satisfy the users "immediate requirements" as well as facilitate our longer term goals.

Opening Statement from Catriona:

  • Week of the 27th to 1st we will get a final list of changes from the users and then address them the next week.

Today's Goals:

  • Figure out what MC4/RC1 is going to be.
  • Determine who is doing what.
  • Determine the documentation (and who is doing it).
  • Need to figure how to use Trac vs. some sort of Project Management vs. Usable Image vs. Tiki vs. Requirements Capture/Sharing.
  • Naming and release numbering of the software needs to be addressed
  • Web-based marketing front end persona to be fixed (big shinny buttons with "Developers go here", "Users go here", "Download software here", etc).


Brainstorming Session


Note: For clairity, we renamed "RC1" to "Beta1", and agreed to follow the more "traditional" development terms for Alpha, Beta, Release Candidate, Final Release, etc.

What can we add (the "Big List"):

  • Some more file format imports
  • making sure the build system is aligned with the rest of the server
  • adding more functionality to thumbnail browser (replicating some of the data manager functionality to the thumbnail browser)
  • Server installer
  • Client installer
  • Feedback mechanisms
  • inline help system
  • accelerator keys
  • tab ordering
  • User Admin system (add/modify/delete users)
  • Calculate (and maybe store) a projection
  • Cell Profiling
  • Measurement tools
  • Demo server? Laptop single install of both client and server
  • Compression Library
  • Client look and feel (unifying the icons, etc).
  • Exporting to OMETiff and downloading the archived original files
  • adding the acquisition date to the file, original file path, etc.
  • displaying the remaining free disk space in the client
  • Expand the amount of meta data we expose (and where / how we expose it)
  • Improving timing information in the image viewer
  • Channel annotations
  • Customer support?
  • Tracking downloads and feedback (register for downloads?)
  • Rendering functionality maybe needs a change (change revert features)
  • RC1 installation testing
  • Drag and Drop functionality
  • Point measuring tool
  • What is our release strategy (email everyone!!)
  • Redo of the openmicroscopy.org website to make it more of a portal
  • icons, branding, etc.

Deciding who does what:

  • No major surprises for holiday takers. Most around the week between Xmas and New Years


Organized Work List

Developers List for Beta1 Release:

  • too many open files (file handle garbage collection) fix (finally)
  • importer must be moved into the build system (Brian)
  • expert analysis of the Shoola and Importer UI (David)
  • some minor functionality changes will be added to the thumbnail browser (Brian/Jean-Marie/Donald)
    • tabbing order needs fixing in shoola (fix tabbing in the browser's tree view)
    • some minor look and feel tweaks
  • big endian and off by one errors (Brian)
  • server installer (Chris/Brian/Donald/Jean-Marie)
  • (Jean-Marie: please fix debug box size on the shoola client)
  • feedback mechanism (Brian/Donald)
  • too many open files (Chris)
  • User Admin system (Brian/Donald/Chris)
  • Need to add jar hash signatures and version error trapping (Josh/Jean-Marie/Brian/Donald)
  • remove archiving button from importer till beta 2 (Brian)
  • adding acquisition date to the file, original file path, etc. (Josh/Jean-Marie)
  • displaying the remaining free disk space (Jean-Marie)
  • add functionality to server so you can move the ome repository to a different location (Chris/Josh)
  • sanity check the server from the admin tool (Donald)
  • handle the first time loading postgres error in shoola (seems OK with importer) (Josh/Jean-Marie)
  • (Brian/Josh: change the OriginalFile.size from Int to Long)
  • Beta1 installation testing
    • Laptop single install
    • Vanilla Linux install
    • Vanilla Mac OS X install
  • Confirm that there are no outstanding blocking tickets for dependencies (Josh)
  • Test server/client build with Derby/HSQLdB and VM bundle for turnkey solution (Chris)
    • If we offer this, how do we handle database migration

Non-Developer list:

  • release strategy statement. Who its being released too, etc. (Jason)
  • redo the openmicroscopy.org website to make it more of a portal (Jason/Brian spearheading*meeting next week)
  • community page / forums for feedback
  • Customer support: Buy server. PHPBB, etc.*icons, branding, etc. Naming, release numbering, etc.
  • Tracking downloads and feedback
  • documentation (David/Brian)
  • Tiki updates (Josh) and synchronization with Shoola "build" doc system (Jean-Marie)
  • Javadoc (Chris/Josh)

Usable Image List:

Beta1 Tickets:

  • Expert Walkthrough / Heuristics (David)
  • Help System (PF/DS/BL)
  • Paper Prototyping Workshop (DS/PF)
  • Logo design (Andrew Cook)

UI Jobs:

  • Video output and upload (General populate UI website) (Catriona)
  • Use Case writing (and gather and reformat OMERO UCs: NB consider where to store this stuff) (David)
  • Scenario writing & workflow mapping (Catriona)
  • Persona writing (Paula)

Post Beta1:

  • Feedback Analysis and reporting (Paula)
  • Visualization research (David)
  • Collaborative working / Ontologies research (Catriona)


Future Plans


RC1 & 3.0 final (February 1 & March 1)

  • start the 3.1+ stuff in a branch
  • writing papers (beginning of year)
    • 1+ papers from UI
    • 2+ papers from dev. (bioinfo. java infrastructure & rendering/PGI, etc.)

3.1+ (Beyond March 1)

NOTE: S+ items require server changes (1 known, 5 need requirements)

Priority 1 Items

  • RC1::DATA MIGRATION TOOL!!!
  • Existing work
  • Indexing (S+)
  • Server side importing
  • top-file types ~10 (import)
  • testing suite
  • projections (derivate images)
  • adjusting RE for out-of-range

Priority 2 Items

  • cell profiler plugin
  • Integration with OME-XML

Priority 3 Items

  • ROIs (S+)
  • Hi-Browser (drag-n-drop,...)
  • Validation (S+)
    • Not a user visible change, but one that directly affects all users. Currently a significant percentage (20-30%) of the model UML is NOT implemented in the server. These are constraints that don't take place at the SQL level and need code. This code possibly go hand-in-hand with Josiah's idea of various spec-levels. (Josh)
  • Working Sets (S+)

Priority 4 Items

  • screening model (screening-cognizant app., updating ui for plate,...)(good for Michael)
  • supporting mass spec., etc.

Priority 5 Items

  • Scripting & Work flows (S+)
  • Lab Notebook (S+)
  • Flexible annotations (S+)
    • Allows .txt/.html/.xml/.pdf/.doc/... to be attached to nearly anything
    • in combination with Lab Notebook — similar model needed
  • Events/Provenance (History/Versioning/Audits) (S+)
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