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openworm/neuronal-analysis

Tools to produce, analyse and compare both simulated and recorded neuronal datasets

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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

Stephen Larson

@slarson

Thanks for making that waffle board @theideasmith. Was just updating it.

Akiva Lipshitz

@theideasmith

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:

Akiva Lipshitz

@theideasmith

Three State Model on Multiple Graph Types, with same number of nodes

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?"

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