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    Michael Currie
    @MichaelCurrie
    just play with the w object in your python shell to see what's possible
    Your task to complete the issue openworm/tracker-commons#113 would be to write a function that can take such a w object and output a valid BDML object.
    So by doing this, I've saved you half the effort (loading WCON).
    So you won't have to puzzle over the nested format of WCON at all.
    Hope this helps! Let me know if you need anything else.
    Michael Currie
    @MichaelCurrie

    Hey @aexbrown @ichoran @ver228 @Eviatar here is OpenWorm senior contributor Balázs Szigeti's omega turns survey: ​http://groups.inf.ed.ac.uk/worms/index.html

    Please consider participating!

    Eviatar
    @Eviatar
    Hi, I took the survey and have some strong thoughts on omega turns. So here we go:
    1. Worm literature is notoriously poor in defining behavior. We have a strong definition for pirouettes at http://www.wormbook.org/chapters/www_behavior/behavior.html#sec7_6
    But it's a weird and forced definition.
    Worse yet
    From Wormbook "Some researchers include omega turns as reversals. And, some researchers count increased backward locomotion as a reversal or response; most do not. A precise definition of the behavior to be scored is critical for analysis."
    Generally, behavior has been a fudge and we need stronger definitions.
    Stephen Larson
    @slarson
    (cc: @balazs1987)
    Eviatar
    @Eviatar
    1. Andre defined upsilon turns to differentiate less sharp turns that are not omega turns but we really should just quantify omega-like turns with a histogram to see what the distribution is. If it's clearly unimodal, we need a new definition. Otherwise, we can strike a threshold using the histo.
    Should've been labeled #2. Is Gitter autocorrecting me?
    Sorry Stephen, should I move the convo elsewhere?
    Stephen Larson
    @slarson
    I think it thinks that is markdown, Ev
    No no, this is good!
    Eviatar
    @Eviatar
    Great!
    Continung.
    Stephen Larson
    @slarson
    I just want Balazs to see it
    Eviatar
    @Eviatar
    1. The list of videos is quite interesting. Sometimes the worm touches itself & sometimes it doesn't but comes close. For me, an omega turn is a ~180 degree reorienting event that uses proprioception to determine the opposing direction. Do we need touch to do this? How about just the wave of food/media motion that can be felt as the worm approaches its tail compressing the media between its 2 extremities? And, maybe my definition isn't teh popular one?
    Arggghhh. That was #3.
    Moreover, sometimes an omega is preceded by reversal. These are clearly conjoint behavior and they should have their own name when coupled.
    Furthermore. Often the omega is a smooth turn but, in the videos, some omega-like turns are interrupted by foraging (is this a mutant?), defecation, and other non-smooth perhaps independent behavior. If we consider these non-omega turns we may lose mutant behaviors that decoupled omegas from their smooth execution. On the other hand, these may truly not be omega turns. We need to make a hard choice here.
    Eviatar
    @Eviatar
    Finally, how do we classify omega turns in unc mutants? I would prefer a definition that is, as much possible, robust against locomotion defects. But, this may indeed be impossible.
    I'll let Andre weigh in. He may have strong opinions having faced this problem multiple times.
    Chee Wai Lee
    @cheelee

    I'll need to follow up (as best as I can given a lack of access to published literature) with the cited publications, but has there been any other comprehensive large-scale data analysis work on worm movement like in Andre's paper http://biorxiv.org/content/early/2015/04/08/017707 ? Naively it feels to me that an often repeated sequence of shapes-over-time can be used as a context-neutral method to further characterize context-sensitive movement behaviors such as the Omega (full disclosure: I have no clue what is meant by an omega turn.)

    The reason I asked is because in my previous field of application performance analysis, a very similar problem plagues the research community where characterizing the (high level) "behavior" of various scientific code kernels is concerned.

    balazs1987
    @balazs1987
    hey Ev,
    thank you for your comments
    generally we are in agreement
    regarding the difficulties in defining what is an omega turn

    In my last paper (http://rsif.royalsocietypublishing.org/content/12/113/20150899) I have argued that behaviour is not a set of discrete states, but rather a continuous spectrum. When presenting my results people often assigned the observed continuity as an artefact of my method rather than as a feature of behaviour. I have been criticized that other omega turn detection algorithms or experts could pick out omegas unambiguously.

    I wanted to put this claim to the test and this survey is a part of this effort. I have already compared 4 omega turn detection algorithms (Laurent 2015, Yemini 2013, Huang 2006, Salvador 2014) and they often have a disagreement for over 50% of the events!!! I am just collecting the expert annotation now, but based on what i have seen so far that is going to be pretty diverse as well.

    By highlighting that neither expert annotation nor the algorithms are consistent with each other I hope to emphasize that behavioural annotation is actually inconsistent in the literature. Furthermore I think that if we can not agree on an omega detection algorithm and expert opinion is diverse as well, then that would be a strong argument to consider the 'behaviour is a continuous spectrum' framework as an alternative to the currently dominant 'behaviour is a set of discrete states' paradigm.

    one more thing: if you could invite your lab members to the surve I would be very grateful
    I had many responses from PI's, but for some reason it seems that people have not forwarded the invitation to grad students in their labs
    Stephen Larson
    @slarson
    (cc: @Eviatar )
    Michael Currie
    @MichaelCurrie
    Hey guys we are meeting now on Google Hangouts. Let me know if you need the link
    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?