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    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!!
    Michael Currie
    @MichaelCurrie
    [Stephen Larson, OpenWorm Foundation] Question guys that @a-palyanov is interested in. We've seen this excellent movie online: https://www.youtube.com/watch?v=x861P1ijpR8 -- Do you think it is possible to process this movie via the movement-validation pipeline? Is it possible to augment the pipeline to also be able to extract the values of the calcium signal in the muscles, such that we would have a value of activation per muscle over time? cc: @jimhokanson @aexbrown @kezhi
    [Andre Brown, OpenWorm Foundation] Definitely possible to run through feature pipeline and to extract fluorescence levels. Muscle activity not directly related to fluorescence because of sensor kinetics, though some of that is addressed in this paper: http://www2.mrc-lmb.cam.ac.uk/groups/wschafer/2015-1.pdf
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] FYI, André, Chee Wai, Avelino and I just had a meeting to figure out some of the cloud-related issues that need to be resolved.
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] We've decided to make this a weekly meeting until the replication paper has been released. To be included just ask Chee Wai or I.
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] @cheewai1972 I was thinking of starting a new web server for movement.openworm.org. It has been backed by an m4.large instance until February 2017 when I turned it off since we lost AWS funding and it was costing $0.20 per hour ($150 per month).
    [Michael Currie, OpenWorm Foundation] Pasted image at 2017-04-17, 8:36 PM
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] I am going to put it on a t2.medium "on-demand" instance, $0.047 USD per hour ($35 USD per month). It's half the RAM at 4 gigs instead of 8 gigs for m4.large.
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] Hi @aexbrown here is the list of features to to obtain your top 10 from: https://github.com/openworm/open-worm-analysis-toolbox/blob/master/documentation/Yemini%20Supplemental%20Data/ReadMe.md
    [Michael Currie, OpenWorm Foundation] André, Chee Wai, Rex, Avelino, and I just had our monthly standing meeting. Notes are here: https://docs.google.com/document/d/1hfvrYRapmuBRyowVT9ILAjq2NNu3csuR0hiyzdx6b8w/edit?usp=sharing
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] Our next standing meeting is on 19 May 2017 at the same time (16:00 UTC).
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] (Had to change the date of the meeting due to a conflict, please note it is now on 25 May)
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] @aexbrown please let me know how you would like the Zenodo upload to look. I uploaded the 5 file payload to the sandbox: https://sandbox.zenodo.org/record/71862#.WP3k8dKLSM8
    [Michael Currie, OpenWorm Foundation] Basically I'm wondering what your thoughts are about naming, and what would be in the description. Should we have the whole metadata there? Right now it's just the keys in the database, which are not very informative.
    Michael Currie
    @MichaelCurrie
    [Andre Brown, OpenWorm Foundation] Cool, nice to see what a zenodo page looks like. It would make sense to have most of the metadata there. At least the strain, gene and allele (where available), time stamp, sex, and condition (i.e. on food or not) would all be useful to have as a quick summary for anyone looking at the data directly on the page.
    Michael Currie
    @MichaelCurrie
    [Chee Wai Lee, OpenWorm Foundation] @aexbrown @mcurrie Pretty bad thunderstorm here, I might cut out and lose internet connection or power. If I don't get on the Hangout, that's probably what happened.
    Michael Currie
    @MichaelCurrie
    [Michael Currie, OpenWorm Foundation] I will be 5 mins late sorry
    Michael Currie
    @MichaelCurrie
    [Chee Wai Lee, OpenWorm Foundation] @aexbrown @mcurrie I got a preliminary documentation for the tool written up in the dev branch of the repo. README.md is the master document for this. Please let me know what you think. Thanks! https://github.com/openworm/movement_cloud/tree/dev