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    Michael Currie
    @MichaelCurrie
    I've put an issue up on the OWAT repository for this: openworm/open-worm-analysis-toolbox#189
    @Eviatar I'd appreciate any help you can offer here in identifying what needs to be ported.
    thanks!
    ido77778
    @ido77778
    Hello, I am new to the open Worm project and I want to help around here as I will have some free time in the coming months. I know Python and C++, so I believe I have the nessasry
    Necessary* Skillset. I have been told to go he in the main Chat... So how can I be of help, do you have any beginner project/tasks?
    Michael Currie
    @MichaelCurrie
    Hi @ido77778 ! There is a project-wide effort to flag certain issues as "well-specified" so they can be handled by someone not familiar with any context about the project. For now the best candidates are openworm/tracker-commons#100 and openworm/tracker-commons#113
    For #113, I agree with your suggestion that converting from WCON to BDML will be easier than the reverse, so if you start with that it would be awesome!
    You'll probably still have questions - if you do please feel free to set up a quick meeting by google hangouts with me using http://www.meetme.so/MichaelCurrie
    Or just chat away on here if you prefer
    Cheers! Thanks for your interest!
    ido77778
    @ido77778
    @MichaelCurrie Well, I don't have any questions right now so I'll start working right away. Anyway, thanks for the help and if I'll have any question I will probably ask it in this chat.
    ido77778
    @ido77778
    @MichaelCurrie I have a question about outputing the data as an ordered dictionary... From what I understand the dic cotains subdics, each representing a worm, my question is how those subdictionarys arranged, are the Indexed by timestep (Like BDML)? Or is there some other arrangement? Any way the way to convert the data to BDML is probably by two nested loops, the outer loop loops over the worms and the inner loop loops over the data and generates the XML file.
    ido77778
    @ido77778
    The biggest issue is the fact that BDML requires a sort of graphical representaition for each object, which means we must create one for each worm, proceduraly. Cronin, Et al. create such a thing by patching together a bunch of lines, I hope Dr. Ken Ho can help us with such a thing.
    Michael Currie
    @MichaelCurrie
    Hi @ido77778! The format is discussed in detail here https://github.com/openworm/tracker-commons/blob/master/WCON_format.md and the schema is here. The part of the schema relevant to your question is the "data" part.
    However, rather than writing a tool to parse WCON files yourself, I highly recommend you use https://github.com/openworm/tracker-commons/tree/master/src/Python or one of the other languages available here: https://github.com/openworm/tracker-commons/tree/master/src.
    I wrote the Python version and I can say that you would do something like import wcon; w = wcon.WCONWorms.load_from_file('test_file.wcon')
    then, you can access the worm's data as a pandas dataframe.
    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