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  • 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
Akiva Lipshitz
@theideasmith
Yeah
Stephen Larson
@slarson
OK — hangout in like 10 minutes?
Akiva Lipshitz
@theideasmith
My previous message didn't go through. I'm not able to talk today. Monday?
Stephen Larson
@slarson
Ah sorry about that! No worries. Monday is tight for me; Friday is safest to plan for now but maybe we can do something ad hoc on Monday
Stephen Larson
@slarson
@/all sent an invite for Friday at 2pm ET for a chance to sync. If others want to join, just message me here in the channel
By the way, found this paper and it seems really relevant: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000190
Akiva Lipshitz
@theideasmith
@slarson can you resend the invite?
Stephen Larson
@slarson
Yes; doing now
Stephen Larson
@slarson
Thanks for making that waffle board @theideasmith. Was just updating it.
Akiva Lipshitz
@theideasmith
timeseries0.jpg
Initial simulations of model used in Organization of Excitable Dynamics in Hierarchical Biological Networks
Luke Czapla
@lukeczapla
It's pretty interesting results and I just made a minor change to align the model exactly with the paper. I haven't had luck with PyOpenWorm so the CElegansNeuronTable.xls was used here. I think tuning simple models with experimental data is a good plan to demonstrate the proof of principle but this one is too simplistic. If individual neurons at least had a few parameters (individual f and p values is a good start - it'd give a coarse-grained picture of neuronal excitability and recovery) then we could extract information by fitting to the kato data and do a full scientific simulation study
Stephen Larson
@slarson
@theideasmith @lukeczapla Wow :) OK we should find a time to get together and discuss these. This week I’m all booked up; how’s your next week looking?
Akiva Lipshitz
@theideasmith
Any day next week
Akiva Lipshitz
@theideasmith
The model I used to generate the figure above was written incorrectly. Here's what it really should look like:
timeseries.jpg
Akiva Lipshitz
@theideasmith
Three State Model on Multiple Graph Types, with same number of nodes
Multiple_Graphs_Sim.jpg
Stephen Larson
@slarson
I totally want to know more!
Ok @lukeczapla any constraints on day next week?
Akiva Lipshitz
@theideasmith
/all any time to meet tomorrow or Friday?
Stephen Larson
@slarson
Hey hey you should have an invite from me already
Maybe i sent it to the wrong address?
It is for friday 3pm ET
Akiva Lipshitz
@theideasmith
Ok great
Stephen Larson
@slarson
@theideasmith @lukeczapla ready when you are
Stephen Larson
@slarson
@theideasmith @lukeczapla Sorry we couldn’t connect today
Luke and I were chatting a little on here
He was saying:
@lukeczapla
yes, I think we could come up with a scan of all of f and p space
there are some neurons (<20) that they took out of the model, other than that it should be the same thing
Maybe let’s kick back and forth where we are on here
Luke Czapla
@lukeczapla
that's for comparison to the paper
Stephen Larson
@slarson
I’d still be up to sync for an hour over the weekend if there is a better time
Akiva Lipshitz
@theideasmith
Unfortunately I was stuck in a lab meeting that ran far longer than I expected. I'm sorry I missed it.
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?"