Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • May 22 16:55
    clausagerskov closed #172
  • May 18 21:23
    ido4848 commented #141
  • May 18 21:22
    ido4848 commented #144
  • 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
Sergey
@skhayrulin
@slarson little update
This message was deleted
it is about memory root@sibernetic-vis-8e-5-1:/# df -h
Filesystem Size Used Avail Use% Mounted on
none 500G 35G 441G 8% /
tmpfs 30G 0 30G 0% /dev
tmpfs 30G 0 30G 0% /sys/fs/cgroup
/dev/xvdb 500G 35G 441G 8% /data
shm 64M 0 64M 0% /dev/shm
This message was deleted
simulation step
[[ Step 462541 ]]
_runHashParticles: 12.744 ms
_runSort: 109.693 ms
_runSortPostPass: 15.604 ms
_runIndexx: 5.338 ms
_runIndexPostPass: 0.425 ms
_runFindNeighbors: 238.541 ms
_runPCISPH: 772.026 ms 3 iteration(s)
membraneHadling: 39.661 ms
_readBuffer: 1.237 ms
so I actually wait that it will finish tomorrow
Sergey
@skhayrulin
Hi @/all it looks like sibernetic finished run on cluster see picture here @slarson should I terminate cluster node or we firstly should download data from it?
Stephen Larson
@slarson
OK so we should have gotten the data going today — @skhayrulin did it work to get it off via dropbox?
Sergey
@skhayrulin
Ok all it's fine
I've just finished with uploading data in my dropbox total size it's 11Gb
I'm now terminating node
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
This message was deleted
This message was deleted
This message was deleted
This message was deleted
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