Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Jun 03 2019 21:43
    Uiuran commented #15
  • May 28 2019 12:58
    Uiuran commented #15
  • Mar 05 2017 06:18

    theideasmith on master

    updates to graph drawing algori… (compare)

  • Mar 03 2017 22:12

    theideasmith on master

    beginning study of neural field… Merge branch 'master' of https:… (compare)

  • Dec 19 2016 18:18

    slarson on master

    importing experiment to graph N… (compare)

  • Sep 19 2016 16:30

    slarson on master

    Create .openworm.yml (compare)

  • Jun 15 2016 12:06
    theideasmith commented #17
  • Jun 14 2016 18:40
    lukeczapla commented #17
  • Jun 14 2016 16:15
    theideasmith opened #17
  • Jun 13 2016 15:36
    theideasmith labeled #16
  • Jun 13 2016 15:36
    BenjiJack opened #16
  • Jun 05 2016 18:17
    slarson commented #14
  • Jun 05 2016 18:16
    slarson commented #14
  • Jun 05 2016 13:52
    theideasmith commented #14
  • Jun 03 2016 15:11
    theideasmith commented #14
  • Jun 03 2016 03:15
    lukeczapla commented #15
  • Jun 02 2016 16:08
    theideasmith commented #15
  • Jun 02 2016 16:05
    theideasmith commented #15
  • Jun 02 2016 02:20
    theideasmith commented #15
  • May 25 2016 17:53
    theideasmith edited #15
Stephen Larson
@slarson
Lab meetings do that :)
Akiva Lipshitz
@theideasmith
Than
Stephen Larson
@slarson
Do you guys have time tomorrow?
Luke Czapla
@lukeczapla
how is everything going akiva?
well tomorrow night is possible, but sunday usually better
Akiva, did you look into the scanning of "f" and "p" space of the 3 state model?
Stephen Larson
@slarson
I could do Sunday
Luke Czapla
@lukeczapla
if Akiva hasn't done it yet we could set up that scan, it's presented in the paper. Stephen can you identify the neurons they took out? The pharyngeal ring neurons
Stephen Larson
@slarson
Yeah, the pharyngeal ring neurons — what do you want to know about them? The names?
Luke Czapla
@lukeczapla
yep, the names - they were removed from the system in the paper
Stephen Larson
@slarson
See if this loads up for you: should be our master cell list filtered down for just the pharyngeal neurons: https://docs.google.com/spreadsheets/d/1NDx9LRF_B2phR5w4HlEtxJzxx1ZIPT2gA0ZmNmozjos/edit#gid=1&fvid=812791088
Akiva Lipshitz
@theideasmith
Yeah I haven't done the parameter space scans.
I could do anytime on Sunday. I don't think it would be a good use of your time to meet again if there was a meeting today. What came out of the meeting today? Where are we right now?
Stephen Larson
@slarson
No we didn’t do the meeting today; we were just pm’ing on here
I think getting the time to jump in a hangout will help us all to answer exactly that question
“Where are we right now?"
Akiva Lipshitz
@theideasmith
Ok ok
Stephen Larson
@slarson
Alright so @lukeczapla what time is good?
Luke Czapla
@lukeczapla
Let's talk tomorrow at 1pm
this looks exactly right in terms of the amount of neurons they removed
Stephen Larson
@slarson
Sounds good!
Stephen Larson
@slarson
Marder, E., & Taylor, A. L. (2011). Multiple models to capture the variability in biological neurons and networks. Nature Neuroscience, 14(2), 133–138. doi:10.1038/nn.2735
Stephen Larson
@slarson
Kaiser, M., & Hilgetag, C. C. (2010). Optimal hierarchical modular topologies for producing limited sustained activation of neural networks. Front Neuroinformatics, 4(May), 8. doi:10.3389/fninf.2010.00008
Check out this book: https://drive.google.com/open?id=0B_t3mQaA-HaMdFdGeFcxNEstZUU in particular the introduction, chapter 18 and chapter 10
Stephen Larson
@slarson
@lukeczapla @theideasmith you guys around?
Akiva Lipshitz
@theideasmith
Sloppy Models: relevant for thinking about criticality space? http://arxiv.org/pdf/1501.07668v1.pdf
Stephen Larson
@slarson
Hello — looking to see what availabilities are to look further into how to fix issues with c302 that @lukeczapla and @theideasmith ran into. I know @pgleeson is travelling abroad right now — let’s talk about when we could get together to resolve the issues
Stephen Larson
@slarson
Akiva Lipshitz
@theideasmith
Hi everyone – it''s been a while since this neuronal analysis has been in motion. How are you all doing?
Stephen Larson
@slarson
On this front, not as much @theideasmith but we've had more activity at the channel and single cell model level recently. If you want to get plugged in we'll have a session 9am PT on Friday. Cheers!
Stephen Larson
@slarson
@raminmh @lungd In the spirit of making iPython notebooks, I wonder if you guys can try to run this: https://github.com/openworm/simple-C-elegans/blob/master/README.md#quickstart — it should give you an environment you can use to both run and author notebooks and will load up a relevant example on your system
Stephen Larson
@slarson
@raminmh @lungd this: http://hollopeterlab.vet.cornell.edu/uploads/7/3/7/0/73705987/optogenetics_in_worms.pdf is the paper I was referring to today that looks at muscle activation through synapse
Akiva Lipshitz
@theideasmith
I just came across this dissertation about probabilistic methods of analyzing neural spike trains with bayesian inference: http://www.columbia.edu/~swl2133/#thesis.
Stephen Larson
@slarson
Cool :)
How have you been @theideasmith ?
Akiva Lipshitz
@theideasmith
Hi Dr. Larson. Thank's so much for your message. I'm doing well and have finally got back into the swing of things. The first semester I focused on school but now I'm getting back. Incidentally I'm going to be in the lab of Liam Peninski working on state space models for none other than Andre Brown's eigenworms.
Akiva Lipshitz
@theideasmith
Screen Shot 2017-03-02 at 11.06.22 PM.png
Screen Shot 2017-03-02 at 11.06.13 PM.png
These are some PCA space plots for the data used in the paper http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000028 Dimensionality and Dynamics in the Behavior of C Elegans
The burning question is how to connect them with these plots
Screen Shot 2017-03-03 at 6.09.31 AM.png
Akiva Lipshitz
@theideasmith
@slarson how are you doing? I'm wondering if there are edge weights of the worm connectome. If not, perhaps they can be computed as the covariance of the mutual information between two neurons or something of the like. Why am I asking this? My idea is to find an embedding of the worm's brain in R^3 such that the distance between each node in space is the same as the weight of the edge connecting those two neurons. I then want to fit a surface plot to this embedding and interpret the flow of firing frequencies of neurons through the network as actually being particles moving through a space lattice approximated by the three dimensional embedding which is reconstructed continuously with computational procedures. If I can recreate the surface then one can define such things as "neural field equations" similar to electrodynamical field equations by considering the "potential energy" of a particle at each point on the neuronal space manifold.
Then, you can consider the physical properties of this neuronal space manifold such as
  1. How the neuronal space manifold changes over time
  2. The thermodynamical properties of neuronal space particles
  3. etc
Stephen Larson
@slarson
@theideasmith I’m just seeing this! Holy cow this is cool. Please post over in Slack… we’re not on Gitter much any more! (Public link for folks is here: http://openworm.slackarchive.io/)