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  • Mar 10 11:18
    pgleeson commented #176
  • Mar 10 10:28
    pgleeson opened #177
  • Mar 09 09:42
    woobin3069 commented #176
  • Mar 09 09:13
    woobin3069 commented #176
  • Mar 08 03:14
    mwatts15 commented #176
  • Mar 08 03:13
    mwatts15 commented #176
  • Mar 08 01:27
    woobin3069 opened #176
  • Feb 05 08:10
    skhayrulin labeled #171
  • Feb 05 08:10
    skhayrulin labeled #171
  • Dec 08 2020 09:37
    md-121 commented #168
  • Nov 18 2020 12:28
    waayst closed #175
  • Nov 18 2020 12:27
    waayst commented #175
  • Nov 18 2020 09:36
    waayst opened #175
  • Oct 23 2020 18:53
    fix27 edited #174
  • Oct 23 2020 18:53
    fix27 commented #174
  • Oct 23 2020 18:53
    fix27 commented #174
  • Oct 23 2020 18:38
    fix27 edited #174
  • Oct 23 2020 18:16
    fix27 opened #174
  • Oct 17 2020 12:43
    clausagerskov closed #173
  • Oct 17 2020 12:43
    clausagerskov commented #173
Stephen Larson
@slarson
@skhayrulin OK great
Stephen Larson
@slarson
@a-palyanov @skhayrulin I’m pretty curious if the results are usable :)
Also, any thoughts on #102 ?
Stephen Larson
@slarson
@skhayrulin How are the results looking?
Sergey
@skhayrulin
it's better to ask @a-palyanov he's been working with it from tomorrow
Stephen Larson
@slarson
@a-palyanov any update?

@dillmann asks (about Sibernetic:)

I've toyed around with this a bit and have been modifying the inputs for the muscle activation variables. I understand that it uses a Python object (which gets its inputs from a .dat file) to specify the level of muscle activation.
Queries
I believe there are 95 Somatic muscles in C. Elegans but here we are representing 96. Further inspection shows that the NeuroML model (which we intend to connect) also generates output for 96 cells. Is this to be consistent or change? How will this affect how the Sibernetic worm model is generated?

I’ll let the other guys weigh in, but my memory is that the 96 was a first run kind of thing because it was an even number, and that we were eventually going to take it back out again when we got closer to the end because it presented some significant extra work to take the last one out. @skhayrulin and @a-palyanov please weigh in :)
Stephen Larson
@slarson
Welcome to @tessbianchi who is also having a look at openworm/OpenWorm#177
a-palyanov
@a-palyanov
There are 96 muscles in the current C. elegans body model in Sibernetic, because left/right and up/down symmetry is quite convenient and I used the data for only one of 4 muscular quadrants to generate all 4 of them. Here is the schema of body wall muscle cells layout in C. elegans body: http://www.wormatlas.org/hermaphrodite/musclesomatic/Images/musfig15leg.htm
According to it we can just ignore the 22-th muscle in VL quadrant and send the signals which should go to MVL22 and MVL23 to 23-th and 24-th muscles
a-palyanov
@a-palyanov
Of course it is possible to define geometry for all 4 muscular quadrants indiviaually and make 95 muscle cells, but it requires the data about all these cells geometry.
By the way, I used this figure - http://www.wormatlas.org/hermaphrodite/musclesomatic/Images/MusFIG7lr.jpg , DL quadrant, to get the muscle cells geometry which is currently used in Sibernetic C. elegans body model.
Stephen Larson
@slarson
Great answers @a-palyanov !
What’s new @a-palyanov and @skhayrulin ?
a-palyanov
@a-palyanov
Finally I've got new results on swimming at different viscosities.
Is there a way to upload images from a local PC here?
a-palyanov
@a-palyanov
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Link leads to high-res image
a-palyanov
@a-palyanov
I think it's a good idea to display the trace of the worm tail and center of mass when visualizing worm movement.
Stephen Larson
@slarson
@a-palyanov you can drag / drop images into gitter
This seems promising; i'm about to sleep now but will look in detail in the morning
a-palyanov
@a-palyanov
Thanks, Stephen!
Stephen Larson
@slarson
Very cool. Do you think it is possible to estimate the wavelength and frequency in those three viscosity conditions @a-palyanov ?
a-palyanov
@a-palyanov
Sure. It shouldn't take much time.
a-palyanov
@a-palyanov
For viscosity = 1.0e-04 frequency = 1.7 and wavelength = 0.8. For 2e-4 and 3e-4 frequency is the same (I didn't changed it) and wavelength is a bit larger because amplitude is lower.
Stephen Larson
@slarson
Screen_Shot_2015-09-22_at_8.52.10_PM.png
Interesting. Frequency of 1.7 is right on the money for swimming.
Wavelength looks more like crawling though...
Stephen Larson
@slarson
Hey there @a-palyanov
a-palyanov
@a-palyanov
Hi @slarson
Stephen Larson
@slarson
@skhayrulin — just pinging you in case you are around
First of all; we should probably set up a new session for next week to chat via hangouts
Do you think you can fix the webcam issue by then?
a-palyanov
@a-palyanov
It works already. Tried another usb slot
Stephen Larson
@slarson
Oh yes, shall we go back in?
a-palyanov
@a-palyanov
So we can return to hangout
David Simeroth
@davidsimeroth
Hello, everyone! I have a background in fluid dynamics and was wondering what I could help with
Sergey
@skhayrulin
Hi @davidsimeroth nice to hear from you! I think your expirience sold be useful in model validation and testing, if you have any Idea how we can check correctness of our methods (may be some physical tests, actually we have implemented couple but I think it's not enough) it would be great. If you're interest in that we can make hangout meeting where I'll make some introduction into sibenertic and methods inside it
Sergey
@skhayrulin
Sorry I have got a typo I meant your experience "should" be useful
Stephen Larson
@slarson
@pgleeson I know you are on travel. When should we start looking for good times to coordinate a meeting to update progress on c302 / Sibernetic with @a-palyanov and @skhayrulin (and any others like @davidsimeroth @tessbianchi )
Padraig Gleeson
@pgleeson
@slarson I'm back and things are much quieter from 12th July, so any time after that would be good with me.
Deepak Sharma
@dpkshrma
Hello! I just saw a tedx talk about this project.. and am highly intrigued by the complexity of the problem that its aiming to solve. Can anyone spare a minute to let me in and direct me to right place to get started? I am a software dev btw with decent experience in python, JS.
Stephen Larson
@slarson
Hi @/all — please fill out the poll here to sync between @pgleeson @skhayrulin @a-palyanov and myself on c302 stuff. @tessbianchi you are most welcome to join us in this to reconnect with your stuff as well: http://doodle.com/poll/vrt847hdn2bdwdut Others are welcome too, but this one will require some existing knowledge as we are going to want to get into some recent progress