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2011-11-22 Tuesday Meeting

Attending: Jason, Will, Colin, Scott, Andrew, Josh (notes), Chris, Mark, Melissa, Ola (joined 14:35 UK; notes), Carlos (joined 14:39 UK), Curtis (joined 14:40 UK)

Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

Housekeeping Pre-Meeting - 2pm Start

  1. Matters Arising (<10 mins)

    • Josh: ask Chris about VirtualHost - done
    • Ola: link ticket to Alex’s QA or create new ones done
    • Will: ask for timings on SVS files done #7298
    • Andrew: cleanup google docs and define organization - done
    • Will: look at using includes for the training inclusion - ome-xsd browser
    • Andrew: ask Andrew about drupal - Site created by Andrew Millar for us to trial - done
    • Trainers: trying training docs under sphinx
    • Andrew: get Davey on the website - Davey asked to call in for photo by Jason
  2. Email and Forum Review - checked at (5 mins)

    • Email -

      • Leon Kolchinsky - Re: [ome-users] SVS file format functionality problem
    • Forums -

      • Code forum review
        • OMERO.Scripts Restore Colors link
    • QA -
      link

      ID  Status  User/email  Type    Created Selected file   Comment Error
      4047    new i.porter@lif... Insight 4.3.3   2011 11 21  -   When using the paste setting o...   -
      4046    new a.nicolas@du... Insight 4.3.3   2011 11 21  -   A few suggestions: - When impo...   -
      4045    new k.j.z.hands@... Insight 4.3.3   2011 11 17  -   opening a screening image from...   java.lang.Exception: org....
      4044    new k.j.z.hands@... Insight 4.3.3   2011 11 16  -   opening an image from a screen...   java.lang.Exception: org....
      4043    new a.herbert@su... Web 4.3.3-00d1  2011 11 14  -   I had logged on to look at a n...   Traceback (most recent ca...
      4038    new CJW@stowers.... Insight 4.3.3   2011 11 10  -   I am getting a "no processor a...   -
      

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

  2. Movie audit: Colin's presentation (20 mins)

  3. Sprint Status / Branches

    • Proposed for merge-blue
    • Next?
      • Hibernate 3.5
  4. Glencoe Update

  5. Minigroup Updates

    • HIC
    • Model
    • Web
    • FS
    • Usability
  6. Satellite Update

    • "New" Satellites
  7. Java 1.6 (in context of netCDF), see email to nitpick

  8. Encoding 2-d plane information in a URL (from Lee Kamentsky)

  9. Licensing for SCIFIO and OME-XML components (see email to nitpick)

  10. Hiring

  11. Any other business (<5 mins)

    • PRs & screenshots/movies
    • Advertising Docs
    • Use of OMERO by CLS-- a usability project?

Attending

* Jason, Will, Colin, Scott, Andrew, Josh (notes), Chris, Mark, Melissa, Ola (joined 14:35 UK; notes), Carlos (joined 14:39 UK), Curtis (joined 14:40 UK)

Housekeeping Pre-Meeting - 2pm Start

  1. Matters Arising (<10 mins) Started at 14:03 UK

    • Josh: ask Chris about VirtualHost - done
    • Ola: link ticket to Alex’s QA or create new ones done
    • Will: ask for timings on SVS files done #7298
    • Andrew: cleanup google docs and define organization - done
    • Will: look at using includes for the training inclusion - ome-xsd browser
      • Haven’t looked into trac includes. Perhaps wait on sphinx.
      • some work done on ome-xsd
    • Andrew: ask Andrew about drupal - Site created by Andrew Millar for us to trial - done
    • Trainers: trying training docs under sphinx PENDING
    • Andrew: get Davey on the website - Davey asked to call in for photo by Jason IN-PROGRESS
  2. Email and Forum Review - checked at (5 mins)

    • Email -

      • Leon Kolchinsky - Re: [ome-users] SVS file format functionality problem
        • See ticket 7298 above.
        • Chris and Will to define a response.
    • Forums -

      • Code forum review
        • OMERO.Scripts Restore Colors link
          • Andrew to request the script
    • QA -
      link

      ID Status User/email Type Created Selected file Comment Error 4046 (SCOTT) new a.nicolas@du... Insight 4.3.3 2011 11 21 - A few suggestions: - When impo... - 4047 (JM) new i.porter@lif... Insight 4.3.3 2011 11 21 - When using the paste setting o... - 4045 (JM) new k.j.z.hands@... Insight 4.3.3 2011 11 17 - opening a screening image from... java.lang.Exception: org.... 4044 (JM) new k.j.z.hands@... Insight 4.3.3 2011 11 16 - opening an image from a screen... java.lang.Exception: org.... 4043 (JM) new a.herbert@su... Web 4.3.3-00d1 2011 11 14 - I had logged on to look at a n... Traceback (most recent ca... 4038 (JM) new CJW@stowers.... Insight 4.3.3 2011 11 10 - I am getting a "no processor a... -

    • Done at 14:23 UK

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting Started at 14:30UK

    • done
  2. Movie audit: Colin's presentation (20 mins) Started at 14:32 UK

    • Colin: Question from Jean-Marie some time ago

    • Jason: Not just movies on filesystem, but linked to from somewhere

      • Andrew: generated list of movies linked
    • Andrew has tried to support Windows, but no Linux.

    • Chris/Jason: all movies before 4.x; none after

    • Colin: Where else we could use movie? For example, training support. We could also identify training materials and bring up some on-line learning movies.

    • Colin: When we suppose to make movies? Major release, any point of the release, implementation, testing,...

    • Colin: Who will make movies? do we want to have dedicated person/team who will make a movie?

    • Colin: Ready-to-use environment would be useful to make movies. People do not want to spend couple of hours to import images, etc.

    • Colin: Movie content review:

      • Introduction: everyone say ‘hello’ and introduce who the person is.
      • Some time there is reference to other movies, we shouldn’t do it because is difficult to keep track of which movie author refer to.
      • Cleaning db. We should avoid fake entries in environment we use for movie, especially testing entries.
      • We need to make sure client/webbrowser window fully fit into the screen.
      • We need to make sure there are no noises behind.
      • It is nice to see mix of web browsers and OSes.
    • Jason: IE users hit our website the most.

    • Andrew: I was making movie with capturing entire Windows VM desktop. It looks nice.

    • Jason: Comments on numbers. Support people to make movies? But remaking 50 movies is still a lot of work. Maintenance is a huge burden.

    • Will: we have got movies which cover couple of features and some which demonstrate just one thing. I was wondering if your playlist is just another way of organizing them. I guess that sort of type of organization might help with the new release, where we will be able to review what should be recaptured.

    • Josh/Will: just use youtube? Allow people to discover other films.

    • Andrew: it would be nice if we can make youtube-style while you go to end of the movie. If we start using Drupal it will make more sense to find decent media plugin to do it.

    • Jason: We need movie_details file and identify what needs to be redone.

    • Jason: your impression that the pre-4.3 were hopelessly out of date? Colin: no.

    • Need to manage the original files better

    • Andrew: currently we have them on squig

    • Scott: Might be useful to have some of those movies for testing process.

    • Jason: my impression certainly find bugs but it shouldn’t be done for testing process.

      • Colin: there is not problem with making scenario for the movie, which potentially help testing.
      • Jason: how do we standardise databases for making movies?
    • Summary to be turned into tickets:

      • DB setup
      • Scenarios
      • Management of original files
      • All files in one place (youtube?)
      • Colin’s other points.
    • Done at 15:06 UK

  3. Sprint Status / Branches

    • Proposed for merge-blue
      • PR 31 / Ice3.4: Branch has been initially tested, but this is obviously a very large change that will need large scale reviewing. * Josh: time scale depends how long does it take to test it. Ice 3.4 unfortunatly touch everything. We need to retest everything.
      • PR 30 / insight build
        • Will: Does it make sense to have 2 branches: ‘develop’ and ‘everything else’.
        • Josh: We haven’t fully tested. It will make potential problems if we merge with develop.
        • Will: I am not sure how difficult would be making development in my branches and test occasionally it on ‘server’ (not sure that sentence - ola)
        • Chris: If there is anything broken in ‘develop’ there is no way to roll-back. Effectively everyone is blocked then waiting. We could potentially dedicate few people test work as we go.
        • Josh: I would feel safer.
        • Josh: this is the issue with branches which effect the full stack. Have to have a way to do it?
        • Will: I am curios if I could download server pack form Hudson and install Ice 3.4 and got from there insteand of merging.
        • Josh: I have a script for Homebrew to do it.
        • Chris: how many are using homebrew? Will, Simon, Colin
        • Josh: We need to tell everyone if you use Ice 3.4 server you have to use matching clients as well.
        • Chris: maybe today or tomorrow myself and Josh can try it.
      • Josh: any other PR in other branches
        • Andrew: specification folder changes
        • Will: PR 25 more big ROI work.
      • Josh: Since I am in the process of introducing those BIG changes, shall we go and do Hibernate 4.0 as well?
    • Next?
      • Hibernate 4.0
        • Jason: how much work is that and how fare behind we are?
        • Josh: we are on 3.5.6 and we will be jumping straight to 4.0.
    • Done at 15:23 UK
  4. Glencoe Update

    • Done at 15:30 UK
  5. Minigroup Updates

    • HIC
    • Model
    • Web
      • Ola: in process of reviewing/refactoring web tools
      • Working on templates & static media files.
      • Prepare foundation for common application base (cF. extensions)
      • Will: screenshots of templates
    • FS:
      • Colin: There is new branch based on earlier 909 proposal 2
    • Usability
      • Scott: general discussion of tiding up google docs. More active use of alfresco, encouraging presentations, etc.
  6. There were discussion with Jonathan Monk with providing more instances. * Jason: Jonathan is happy to host OMERO instances (pathology/Felts, EMDB, training) * Jason: Possibly for other institutes as well. Who pays the cost? * Josh: does this address monitoring issue. If this goes down they will come back to us, or we need to support it? * Jason: Not decided yet. For medium term, we need to provide some facilities to do it.
    * High-level discussion how clients moving forward, integration and other businesses.

  7. Done at 15:38

  8. Satellite Update

    • ImageJ? Nothing new.
  9. Copyright discussion spiralling into imglib2

  10. Beta release has been pushed back, but now want to have it for the hackathon. Goal: Fiji2 on IJ2

    • "New" Satellites
      • Others have contacted Jason. (cF. German Bioinformatics Network)
    • Done 15:41 UK
  11. Java 1.6 (in context of netCDF), see email to nitpick

    • Curtis sent screenshots of soylatte. Main differences:
  12. fonts are bad if from MacPorts (perhaps X-setting?) * Can’t resize Windows!

    • Jason: can we move to Java 1.6?
      • Curtis: This research was just to see if we can recommend it to people as an alternative.
      • Chris: doesn’t sound like we can. Curtis: certainly not recommended
      • Will: only harming users … if bioformats it’s pervasive. Curtis: but possibly not a GUI issue.
    • 10.5: there is a Java 6 for 64bit.
    • Jason: is it enough time to email people in the mid-June we will switch?
    • Chris: 10.4 hasn’t been updated for 4 years.
    • Melissa: would be reasonable to bundle 1.6 SDK to Insight?
    • Chris: less then 5% use 10.4
    • Jason: Lets email that we will be moving and give potential solutions.
    • Curtis: We could use retrotranslator which allows run compiled code against older Java version. Fiji requires 1.6 for development but use it produce a Java 1.5 jar.
    • Melissa: biggest issue will be netcdf.
    • Chris: would have to be very careful with 1.6 GUI widgets.
    • Jason: first lets review statistics and then provide solution.
    • Chris: we’ll also have Windows users
  13. Encoding 2-d plane information in a URL (from Lee Kamentsky)

    • Curtis: Grant mentioned OpenDAP. Any chance of using that?
    • Will: what are the TODOs/actions?
    • Jason: is it that they don’t want to use OMERO? Curtis: not necessarily
    • Curtis: does this exist? Yes. Using imageId.
    • Will/Ola: There are 2 urls. First image link in WebGateway viewer, second - render image region.
    • Jason: Will, can you respond? OK.
  14. Licensing for SCIFIO and OME-XML components (see email to nitpick) Started at 15:58 UK

    • Latest version from offline discussion between Jason, Kevin & Curtis
    • Jason: need to be careful with the form of the copyright (need to be incorporated)
    • Curtis: e.g. at space science the individuals owned the copyright. Everyone listed.
    • Jason: on some files, OME is listed, but it’s not incorporated. So added attribution.
    • Jason: once legal, needs to be propagated to other parts of the project.
    • Curtis: query into Wisconsin lawyer
    • Chris: should be careful with polluting BSD template.
    • Melissa: those changes are in ‘develop’, shall we merge it with ‘master’?
    • Jason: 3 votes to move this to a branch?
    • Curtis: need to have this for IJ2 beta.
    • Finished 16:13 UK
  15. Any other business (<5 mins)

    • PRs & screenshots/movies
      • Josh: J-M wanted me to mention. Once PR has various tickets from different stories.
      • Chris: discussed in the web meeting.
        • one bug/rfe per component (insight/web/server)
        • same strategy of ticket per bug
      • Finished 16:17 UK (kicked out)
    • Advertising Docs
    • Use of OMERO by CLS-- a usability project?

Action

* Jean-Marie: look into QAs
* Josh: answer https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=919
* Will: ask for the script submission
* Chris/Will: define SVS plan
* Josh: forward Columbus issues.
* Colin: create tickets from movie talk (“Summary to be turned into tickets”)
* Josh: merge-blue with Ice & Insight builds. Hand-off to Chris and homebrewers.
* Josh: start defining short-/med- term monitoring of servers
* Josh: get 64bit 10.5 stats. (Windows users?)
* Will: respond to Grant’s email about the web urls for getting data
* Curtis: resolve WISC copyright rules
* Josh: Add PR/screenshot discussion to next week’s agenda
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