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    Michael Currie
    @MichaelCurrie
    Thanks for attending the meeting on 10 June. I've set the next meeting to be Friday 15 July at 17:00 UTC and sent out a calendar invitation. Andre, Jim, Rex, let me know if this date doesn't work and I can move it.
    Chee Wai Lee
    @cheelee
    @/all Hey guys, this came up during a hangout with Dr. Barry Aprison from the University of Chicago and the Education Committee - do we have any movement datasets where worms are subject to various forms of stress, in particular Osmotic Stress scenarios?
    Andre Brown
    @aexbrown
    @MichaelCurrie I should be able to make it on Friday, but I'll be at a meeting so it will depend on exactly what's going on that afternoon and whether I feel I need to attend.
    Michael Currie
    @MichaelCurrie
    @aexbrown ok no problem. meeting starts in 40 minutes, it may end up being a short one, we can just quickly touch base.
    @cheelee I'm not aware of any such datasets but someone else may know of one.
    Michael Currie
    @MichaelCurrie
    Hi Team, we just had our meeting (Jim and Rex and myself). Here are the minutes: https://docs.google.com/document/d/1qZII5HoKUL2_HrhkFl_t8zblTW9CsCgBCDI3eyHgbIs/edit. See you at the next meeting, on the 12th of August.
    Michael Currie
    @MichaelCurrie
    (I set the next meeting 2 hours earlier than usual to better accommodate our Thai, Singaporean, and British friends..)
    Michael Currie
    @MichaelCurrie
    Hi Team, we just had our meeting (Jim, Rex, Chee Wai, and myself). Here are the minutes. See you at the next meeting, on the 15th of September.
    (note that the next meeting is on a Thursday - not our usual Friday - to accommodate everyone's schedules)
    Michael Currie
    @MichaelCurrie
    @ver228, @aexbrown: FYI we are hoping to get your opinions if possible on any final revisions to the tracker-commons format, at our 15 September meeting, ahead of further publicizing the format. Hopefully WCON will be more "battle-tested" by then since @ver288 will have done plenty of file conversions to that format by then. Thanks!
    Chee Wai Lee
    @cheelee
    I'm getting this weird thing where Travis-CI is reporting testing errors since a few check-ins ago for OWAT, but quite inexplicably github is now allowing me to merge my pull request (of metadata, which shouldn't affect the testing framework at all.) Anyone has any clue what's going on here?
    Michael Currie
    @MichaelCurrie
    Hi Team, we just had out meeting (Jim, Rex, Chee Wai, André, Avelino, and myself). Here are the minutes. See you at the next meeting, on Thursday 13 October.
    Michael Currie
    @MichaelCurrie
    Hi Folks, no one was able to make the 13 October meeting, so I have rescheduled it to 10 November at the same time. You should have a calendar update in your email inbox. See you then!
    Michael Currie
    @MichaelCurrie
    Hello, because of a couple of conflicts from people, I have rescheduled the 10 November to 24 November. You should have the new invitation in your email inboxes. Thanks.
    Chee Wai Lee
    @cheelee
    @MichaelCurrie Saw that. Thanks!
    Stephen Larson
    @slarson
    Hi guys. Was just talking with @a-palyanov and @skhayrulin today. We now need to be calculating wavelength and amplitude of worm swimming and crawling from Sibernetic for the next paper. @a-palyanov had been estimating it from images but now he’s needing to automate this process, and so I thought we should get back to figuring out how to automate this with the software developed here. What is the best bet to get started with this, do you guys think? cc: @JimHokanson @MichaelCurrie
    Stephen Larson
    @slarson
    Screen Shot 2016-11-11 at 8.25.48 AM.png
    This is the output that comes from this
    @a-palyanov would this help?
    a-palyanov
    @a-palyanov
    profiles.png
    @slarson , thanks, but I'm already getting C. elegans body posture profiles directly from Sibernetic after a small modification of its source code.
    Stephen Larson
    @slarson
    cc: @pgleeson
    Stephen Larson
    @slarson
    @a-palyanov and @pgleeson -- @aexbrown is telling me if we can output in the WCON format, then there are a lot of analytics that can be done easily / for free. Can anyone in this channel point to a quick tutorial on how to encode in WCON for these guys? Thanks!
    Padraig Gleeson
    @pgleeson
    Looks good @a-palyanov. How can I get that out of Sibernetic?
    @MichaelCurrie @aexbrown does WCON and compatible tools require points along both edges of the worm or is a midline sufficient?
    Michael Currie
    @MichaelCurrie
    @pgleeson midline is sufficient
    "The body position of an animal is given by x and y. These are typically arrayed and represent points along the midline of the body. "
    ver228
    @ver228
    Hey, I was talking with @aexbrown about adding the dorsal-ventral orientation to the eigenprojections. This is equivalent to multiply by -1 one of the orientations (either dorsal or ventral). For what I understood this is not in the code, but please correct me if I am wrong. I was wondering if the versal-dorsal orientation information is already being used. I think some of the features (bends) should have already incorporated it.
    Michael Currie
    @MichaelCurrie
    From what I understand this is not in the code, as you say. Perhaps @JimHokanson has something else to say though.
    Michael Currie
    @MichaelCurrie
    Hello, the team just had our monthly meeting. Rex, Chee Wai, André, Jim and myself spoke for an hour about the past month's developments. Notes are here: https://docs.google.com/document/d/1hFumS02rujQa_YGC1fBfUV8Dg4WrX057f4NnahEY4rw/edit. The next meeting is on 22 December and is in the OpenWorm calendar. Thanks
    Eviatar
    @Eviatar
    @ver228
    Perhaps I'm misunderstanding but dorsal/ventral have no meaning for eigenworms. I signed features wherein the feature itself had an orientation relative to the dorsal/ventral positions of the worm (e.g., a bend who's convexity was oriented towards or away from the ventral side of the worm -- since worms crawl on their left/right side).
    The eigenworms are a projection into a new linear coordinate system that permits dimensional reduction without losing much data.
    I'm not sure what dorsal or ventral would mean in this context.
    If you change the sign of the eigenworms you will change the loadings in the projection & thereby lose the data necessary to reconstruct the angles of bending along the worm. But the eigenworms are not these angles.
    Eviatar
    @Eviatar
    Generally, I think the eigenworms are a confusing construct & perhaps should be hidden well inside the WCON so that only engineers who really need this data would bother extracting it. I frequently get questions about significance in the eigenworm features & have to explain that they do not easily map to human relatable concepts of phenotype. They were specifically chosen by Andre as a non-biased means of extracting phenotype. The other features we provided are highly correlated with the eigenworms & present a better means of describing phenotypic differences in a human-centric manner.
    Michael Currie
    @MichaelCurrie
    André, Jim, Chee Wai, and myself just had our monthly standing meeting. Here are the minutes of the meeting. The next meeting is Thursday 16 February at 17:00 UTC. See you then!
    Chee Wai Lee
    @cheelee
    @MichaelCurrie I've also made a new pull request to movement cloud with the updated interface features here - openworm/movement_cloud#5
    I'll be developing the skeleton full use-case workflow features in a development branch in preparation for when links to experiment data (on Zenodo) and youtube videos are made available in a new test database. This is outlined in the following issues - openworm/movement_cloud#6 and openworm/movement_cloud#7
    Michael Currie
    @MichaelCurrie
    Hey @cheelee sorry haven't gotten back to you on the above yet... One quick update: I shut down our m4-large ec2 instance to save money as it's costing over $100 per month.. we can perhaps try a free tier instance or starting it when we are using it, at least until we are ready to release it to the public.
    More on this soon!
    Chee Wai Lee
    @cheelee
    @MichaelCurrie Ouch, that's pretty hefty to maintain the prototype interface.
    Michael Currie
    @MichaelCurrie
    Reminder of our monthly meeting, taking place in about 12 hours. Let me know if you need an invite. See you then!
    Michael Currie
    @MichaelCurrie
    André, Chee Wai, Jim, Rex, and myself just had our monthly standing meeting. Here are the minutes of the meeting. The next meeting is Thursday 16 March at 17:00 UTC. See you then!
    Michael Currie
    @MichaelCurrie
    Chee Wai, Jim, Rex, and myself just had our monthly standing meeting. Here are the minutes of the meeting. The next meeting is Thursday 20 April at 16:00 UTC. See you then!
    Michael Currie
    @MichaelCurrie
    (repeating this message for Slack's benefit): Chee Wai, Jim, Rex, and myself had our monthly standing meeting on 17 March. Here are the minutes of the meeting. The next meeting is Thursday 20 April at 16:00 UTC. See you then!
    [Michael Currie, OpenWorm Foundation] Hello all! I've used Sameroom (https://sameroom.io/blog/connecting-a-channel-in-slack-to-a-room-in-gitter/) to connect our Slack and Gitter (https://gitter.im/openworm/open-worm-analysis-toolbox) channels. They will now reflect the same content going forward.
    Michael Currie
    @MichaelCurrie
    [Chee Wai Lee, OpenWorm Foundation] Nice!!