
01:27:00
robert.mcdougal@yale.edu

01:27:07
bill.lytton@downstate.edu

01:27:20
salvador.dura-bernal@downstate.edu

01:27:51
And yes, recordings will be made available after the tutorial

01:34:25
I don't see any specification of numerical method, time step, etc. Where does that happen?

01:34:45
I installed NEURON using the DEB package from the homepage. When trying to load in Python3:ModuleNotFoundError: No module named 'neuron'You need to install from source to use the python interface? Ir should I add something to PYTHONPATH?

01:34:48
https://www.neuron.yale.edu/neuron/static/py_doc/programming/python.html

01:35:41
how many neurons can I simulate using NEURON?

01:36:57
how many neurons: as many as can fit into your computer's RAM. Depends on complexity of your model cells. Tens to hundreds of thousands are easy.

01:37:14
was that olfactory plotting done with h.plotshape?

01:38:03
not sure actually; will have to ask Michele Migliore how that was done

01:38:59
default numerical method, dt etc.: implicit Euler, 0.025 ms. Also available: Crank-Nicholson, and variable-order variable-timestep adaptive integration (you set an error criterion, and the integrator adjusts to meet your spec)

01:40:16
python3 is strongly encouraged ; python2 is gradually going away; 3.7 or 3.8 best

01:41:22
Yeah, pip only works with python3

01:42:15
For Wouter, after installng the .deb file

01:42:34
please use nrniv -python to get the python shell and then importing neuron works

01:42:51
hey for windows, after installing the binary, is the python wrapper installed automatically?

01:46:28
if typing along here omit the 'cell=self' part -- that would only be relevant if within a cell Class

01:46:51
If you are primarily a Python person, make sure NEURON is installed and configured so that you can just launch Python, then import neuron.

01:51:31
i cant import plotly for some reason. can u help?

01:52:32
Do I need to redo the pip install?

01:53:16
What are the x_axis and y_axis?

01:53:34
pip install plotly

01:53:41
to get local plotly

01:53:48
They are the positions in microns

01:53:51
x and y axis are microns

01:53:52
Hi joined just now. Anyone call help me with the commands?

01:53:57
Do you have a doc file containing all the commands you're typing?

01:54:05
do you have plotly running?

01:54:21
let me make a gdoc file now

01:54:54
Thanks Bill!

01:55:07
Please share! thank you!!

01:55:25
Is that possible for us to have the access to the colab file? : )

01:55:49
ps.plot(plotly).show() returns NotImplementedError. What version of NEURON are you using?

01:57:29
Could you leave the commands you type on the screen a little longer?

01:57:40
I get to 50% of the command before you switch

01:57:46
i don't see it yet

01:57:55
what do you mean?

01:58:03
the link, sorry

01:58:14
link to colab

01:58:17
Could you share the colab link Rober now? Thank you

01:58:19
It seems that you have not shared the link in the chat

01:58:21
https://colab.research.google.com/drive/1g09N_uqiPLHjAN1Qpnbx8uKk08Q0QGwc?usp=sharing

01:58:28
thanks

01:58:30
Thank you!

01:58:36
Thank you

01:58:38
looks good!

01:58:44
thanks!

01:59:11
Thank you

01:59:34
is mV the default units?

01:59:47
yes

01:59:58
Thank you

02:00:19
Robert, your battery..

02:00:21
Thank you!

02:00:44
I just downloaded neuron could I have the instructions?

02:01:23
Did you try `pip install neuron` or are you on Windows?

02:02:06
Thank you

02:02:24
Does the nrnivmodl gets installed also through the pip install neuron?

02:02:40
yes that gets installed

02:02:47
Thanks!

02:03:11
i copied all the stuff from robert's colab to https://docs.google.com/document/d/1GCv6JVFX9Zm0wIAcsKaRFlppx9KMPhN7-1p25NqRdx8/edit

02:03:32
it's editable by everyone (in case i fall behind or someone wants to add a useful note or etc)

02:03:33
Can the HH parameters be changed?

02:03:44
yes HH params are accessible

02:03:56
pip install actually works to import neuron directly in python

02:04:52
What Ashraya means is that if you pip install neuron, you can then launch python and inside python do

02:05:01
from neuron import h

02:05:14
That should make pythonistas happy.

02:07:24
mod files are compiled; then launch a version of NEURON with these linked; then access the params from the mod file in python

02:07:41
are MOD files written for specific versions of Neuron?

02:07:47
no

02:08:30
also note that recompile if eg a different OS -- switching from ubuntu 19 to ubuntu 20 for instance

02:09:18
If you update your installed NEURON you have to recompile your mod files.

02:09:42
PointProcess not to be confused with the same name stats concept

02:11:22
._ref_t is not standard python -- this is required since python does not have pointers and pointers are required for NEURON

02:11:44
/cygdrive/d/nrn/bin/nrnpyenv.sh: line 141: /cygdrive/c/Users/RM/AppData/Local/Microsoft/WindowsApps/python3: Permission denied

02:11:49
getting an error

02:12:06
on trying to run when trying to run Neuron

02:12:59
i'm not a Windows guy but aren't the \ different from unix / ??? -- maybe switch to colab for now?

02:13:45
(sorry, but i last used MS OS in the 80s .... - DOS)

02:14:22
its running on an Cygwin (a Linux kernel) within WIndows

02:14:36
uhoh

02:14:48
Local machine issues we'll have to deal with individually after the tutorial.

02:15:19
if you downloaded Anaconda use their powershell prompt it works better than Cygwin I was having issues with that as well

02:15:50
Alison is absolutely right.

02:16:36
(FYI Linux subsystem for windows 10 with xming window manager works like a charm)

02:17:10
Re: continuerun and finitialize, why not just do h.tstop = 10 and then h.run()?? Much less typing, fewer typos.

02:17:29
Wouter's approach is good too.

02:17:39
@Wouter thanks

02:17:46
ill try that

02:17:54
isn't pip there for windows? you can use pip and install neuron .. anaconda is the best for python, either windows or linux.. easy to install all packages needed..

02:18:10
pip install neuron # gives an old version

02:18:25
(problems with 'wheels' which is how these pip install things are built)

02:18:25
i get “notImplementedError” when I run ps.plot(plotly).show(). I have installed pip plotly

02:18:31
me too!

02:19:07
hmm, guess notImplemented could have something to do with how graphics are hooked up on your machine? colab? :)

02:19:20
For now stick with colab.

02:19:34
thank you! will try colab

02:19:41
Otters like 6.3 deg.

02:19:57
Whales and seals are ok with it too.

02:20:27
Could you share it again?

02:20:45
https://colab.research.google.com/drive/1u8jDnCxHfV7E7zCWmAZAu-UEeeffIrcN?usp=sharing

02:20:46
whales and seals are not poikilothermic

02:22:15
weren't you a seal once, wwl?

02:23:15
put colab pointers in the gdoc -- https://docs.google.com/document/d/1GCv6JVFX9Zm0wIAcsKaRFlppx9KMPhN7-1p25NqRdx8/edit

02:25:47
Is delay the sampling rate? sorry

02:26:01
delay is when the Iclamp's current starts

02:26:05
Bill was mistaken for a seal by a shark. :o)

02:26:23
tasteless

02:27:04
h.dt is the "sampling rate"

02:27:06
Typically underscore variables are hidden (pythonic)

02:28:13
the underscore in _ref_ is not for the purpose of hiding anything. it's just syntactic sugar to tell NEURON that _ref_foo means "this is a pointer to foo"

02:29:48
the storage of the time series t and v is implicit. where does it happen?

02:30:03
ok, forgot about that.

02:30:18
the underscores for hidden stuff is actually double underscore eg __add__

02:31:12
as i was saying, h.run()

02:31:17
_ _ ( Indicates special methods defined by the Python language.)(Sometimes used as a name for temporary or insignificant variables (“don't care”).)_

02:31:22
Behind entering … any notes of current tut?

02:31:34
see google doc

02:31:47
https://docs.google.com/document/d/1GCv6JVFX9Zm0wIAcsKaRFlppx9KMPhN7-1p25NqRdx8/edit

02:31:56
Hi, can someone share the link to the collar please

02:32:06
I arrived little late, so can’t see it

02:32:10
Thanks!

02:32:12
https://colab.research.google.com/drive/1u8jDnCxHfV7E7zCWmAZAu-UEeeffIrcN?usp=sharing

02:32:13
the double underscore actually mangles method names, it’s not really recommended ...

02:32:18
Do you have to always type in the units for everything, or is there a way of defining your units in the beginning (if you are using anything other than the default units)?

02:32:27
https://colab.research.google.com/drive/1Ftrq_xQeT6GLMtkn7E_-YUu1wniQlPMY?usp=sharing

02:32:49
Thanks!

02:36:17
I am from a bit different background. This might be a very basic question but don't you need cell body to have the neuron to fire? Can axon "create" a spike from stimulus?

02:36:56
all you need is excitable membrane and a current source

02:37:04
An action potential can occur anywhere in a cell (body, axon, dendrites)

02:37:17
Minhaz you don't need a soma to make a spike as long as the axon has active currents.

02:37:18
not so, nikolas.

02:37:18
In modeling, a compartment is a compartment whether we call it ‘soma’ or ‘axon’. As long as a compartment has some (HH) mechanisms, it can spike.

02:37:41
What Joe said.

02:38:09
Thanks everyone :)

02:40:05
note that "some HH mechanisms" or mere presence of "active currents" isn't sufficient for excitability.

02:42:45
can you elaborate, Ted?

02:43:05
always. but clarity is better than mere elaboration

02:43:22
ok, pedant!

02:43:36
Change my “some (HH) mechanisms” to “appropriate (HH) mechanisms”.

02:43:50
What ted means is that you need active currents, but they need to have the right constellation of parameters ti make the membrane excitable.

02:44:24
strongly recommend study of nonlinear dynamics. richly rewarding.

02:44:28
right, thanks Astrid

02:49:16
http://tinyurl.com/neuron-morphology-example

02:53:39
Using the google collab, executing the 3rd cell freezes the page

02:57:04
When is the next Summer Neuron course planned?

02:57:05
d lamda rule ?

02:57:15
is there a list online somewhere with what is not recommended in new versions of Neuron?

02:57:17
Can you demonstrate a space-time plot in plotly the way NEURON

02:57:28
Freezing Problem does not occur in chrome. Might be firefox problem

02:57:42
d_lambda rule chops each section into pieces that are no longer than a user-specified fraction of the local space constant.

02:57:42
dlambda rule is for determining how many compartment (segments) you need for transfer of a particular frequency

02:58:13
thanks

02:58:20
generally py2 and hoc are not recommended; i may have missed what else robert said not recommended

03:01:53
I think you didn't share it with everyone

03:02:12
http://tinyurl.com/neuron-currents

03:02:19
awesome! thanks!

03:02:20
https://colab.research.google.com/drive/1u8jDnCxHfV7E7zCWmAZAu-UEeeffIrcN?usp=sharing

03:04:08
https://colab.research.google.com/drive/1GqkZmxznrZIWGyM85UynZw2HfSa0K5UR?usp=sharing

03:06:36
Guess: Almost nothing?

03:06:52
can we perform bifurcation analysis in neuron?

03:07:38
can run a lot of sims and graph that but not a formal package for that -- want to write one? :)

03:08:23
will be interesting if there is a way to include xppaut in neuron

03:08:29
That would be cool!

03:09:00
as far as I know, there is no tool like xppaut in python for bifurcation analysis..

03:09:05
i wrote an xpp2mod long time ago but nothing for the aut part

03:09:06
For any desired X, find a Python library that does X, and import it into the same Python session in which you are using NEURON.

03:09:22
yeah that is understandable..

03:09:52
for any Y that is easily said, actually doing Y may be laborious . . .

03:10:16
lol

03:11:41
whats the name of the article showing augmentation in firing rate based in history (under same stimuli=?

03:12:01
WRT d_lambda rule, it's built into the CellBuilder. It is also doable programmatically, but right now I'm only seeing an old example for hoc in the FAQ lilst https://neuron.yale.edu/neuron/faq ("What's a good strategy for specifyingnseg"

03:12:31
I should probbly update that for Python.

03:15:39
how to plot gatting variables for na ,k like m.. ? in neuron

03:15:54
m^3h ?

03:16:31
_ref_m

03:17:21
eg sec(0.5).hh._ref_m

03:17:52
vec.record(sec(0.5).hh._ref_m)

03:18:05
then can plot that vector after running sim

03:21:22
500e6 sec ~16 years

03:23:58
Is the standard used by other simulators?

03:25:25
standard units??

03:25:57
"whats the name of the article showing augmentation in firing rate based in history (under same stimuli=?" Winograd et al. PMID 18474856. See modeldb.yale.edu/144376.

03:26:08
Thank you very much!!

03:27:32
"Is the standard used by other simulators?" Wouter, what standard? You mean d_lambda rule? It's not a standard, it's a robust and effective rule of thumb that produces "sufficient" spatial accuracy in most cases.

03:28:59
@ted: Robert talked about rxd being a standard. Hense my question what are other tools implementing the standard. Answer: Only implemented by NEURON

03:30:35
is there a break at some point? or the lectures are back to back?

03:30:52
yes there is a break planned --

03:31:09
https://colab.research.google.com/drive/1ucFDBRABXJVqZ0OcNweqqNsySbd6lHTk?usp=sharing

03:31:36
Looking at the agenda the break is between 19:00 and 19:00 (not a typo)

03:32:47
concurrency

03:33:13
looking at the schedule for tomorrow, there is, hopefully, a typo that the session starts at 12am :D

03:33:18
tomorrow

03:34:09
Timezone please lol

03:34:17
berlin time

03:34:33
https://cns2020online.sched.com

03:34:36
You can change the time zone on Sched

03:34:49
To wherever you are -

03:34:55
the irony is the first session starts at 12am and the second is at 1pm :D

03:35:21
Time in relative anyway, I understand :-)

03:35:32
:D

03:35:54
As are conduction values

03:36:56
a real computational neuroscientist is impervious to irony

03:37:53
Can the rdx concentrations be coupled between neurons?

03:39:02
the usual coupling is nearest neighbor which you get for free

03:39:47
Ashraya, I think that the 12am is not a typo! looks like it's actually the last event of today - 'today' being relative

03:39:54
Almost neurons in a microcolumn are neighbours I understand. Could you define nearest neighbor in a 3d environment?

03:40:07
adjacency

03:40:22
So all neighbouring neurons in 3d?

03:40:34
adjacency of compartments in space

03:40:52
So the neurons have a shared coordinate frame?

03:41:40
yes

03:42:11
You can use rxd.Extracellular to allow neurons to influence each other via diffusion of rxd.Species in the extracellular space

03:42:37
Ok, then I can ask my original question. How would this work when neurons are distributed on multiple MPI nodes: are the borders transmitted? Is there some shared zone?

03:43:38
for extracellular full space is currently copied and resim'ed on every node -- this needs to be fixed in future

03:43:48
btw, also just in electrophysio world you can identify locations via pt3dadd for every section

03:44:15
MPI works for the electrophys since spikes are sent as events across cells

03:44:48
@Bill lytton thanks

03:46:37
https://colab.research.google.com/drive/1PbQJu6Y66rsp2jhrMiB9V1sQKHZavfmb

03:48:12
Might I suggest that in the end all links are shared in a single document?

03:48:56
great idea

03:48:57
if chat is persistent, does that count as a single document?

03:49:10
lol

03:49:11
I see what you did there.

03:49:27
why other examples not open on rxd ?

03:49:31
if connect and disconnect there is no access to the chat history

03:49:38
that black one

03:49:49
i have been trying to keep up with all links in this gdoc

03:49:56
https://docs.google.com/document/d/1GCv6JVFX9Zm0wIAcsKaRFlppx9KMPhN7-1p25NqRdx8/edit#

03:50:01
not sure i caught all of them though

03:50:27
Thanks

03:50:27
thank you for sharing

03:50:35
One of chat's options (see triple dots) is "save chat". Please please please save chat, Bill.

03:50:38
is editable by all so if i missed anything please add

03:50:54
save chat doesn't work if got kicked out and back in since lost all the early chat

03:51:09
anyone who has been on since beginning please save and then add that at bottom of gdoc

03:51:24
do you have it all ted?

03:51:33
I have all chat, will save everything that now exists just in case I get dropped.

03:51:48
thx

03:52:45
Can we use RxD to model intra- and inter-cellular diffusion in a network model (cell-gap junction-cell)?

03:52:54
yes

03:53:06
Be sure to remine me to save chat again at the very end, just so I'm not distracted by something else.

03:53:16
why other examples not open on rxd ?(other than blue one)..were r their codes ?

03:53:32
@ted remember to save the chat at the end!

03:53:36
We are still in the process of providing tutorials for all the rxd examples, that's why some of the topics don't have links yet.

03:53:52
not now, you mad fool . . .

03:54:05
we are happy to make all stuff public -- yes as adam says some stil cleaning up but if anything particularly interesting then ask us and we can give to you now

03:55:31
I m just asking for information..thanks

03:56:02
More information is always good. Thanks for asking.

03:58:30
Do you have any network stuff planned as well? :)

03:58:48
Great! thanks

03:58:59
where are going to be the recording available?

03:59:06
thanks a lot Robert

03:59:10
I just saved chat up to this point. Passing the baton on to whoever follows the rest of the afternoon.

03:59:30
Thanks a lot

04:00:26
thanks a lot!

04:00:33
for anyone who is new to NEURON, I found this tutorial useful for learning the basics of the GUI, hoc and NMODL. it has 5 parts, first part starts here: http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html

04:00:48
might not be as useful for people who want to work primarily in Python

04:01:20
I generally suggest https://www.neuron.yale.edu/neuron/docs/scripting-neuron-basics

04:01:22
ted -- can save chat now and then again at end of day?

04:01:30
in particular the scripting neuron basics and the ball and stick tutorials

04:01:39
I have added a Links section to our tutorial website that will be updated with video/code/chat links: https://sites.google.com/neurosim.downstate.edu/cns2020-tutorial/

04:01:50
thank you!!

04:03:06
great ! thank you!

04:03:11
great tutorial!

04:06:32
oof

04:07:17
:O

04:07:23
don’t die!

04:07:33
!

04:08:35
No slides?

04:08:37
no presentation window shared?

04:15:13
Is the information added to model db curated or does anything go?

04:16:34
Are models updated with neuron versions?

04:18:20
Do I understand that NEURON does not make changes that would result in different results for modeldb models?

04:19:46
Thank you

04:19:51
Thank you

04:19:59
thank you!

04:20:02
Thanks a lot Robert

04:20:19
yes

04:20:21
Awesome session thanks so much!

04:20:27
not breaking ModelDB NEURON entries: generally, yes, what worked before should continue to work, but there are occasional changes

04:20:29
Thank you, Robert!

04:20:34
yes

04:20:55
Thanks! where will we be able to access the recording for this tutorial after it is over?

04:20:57
@ RObert thank you for the answrs

04:21:09
Thanks Robert!

04:21:31
ModelDB requires models to be associated with a peer reviewed publication. New NEURON versions are tested on a large subset of the NEURON models in Modeldb in an effort to retain backwards compatibility

04:21:53
we’ll put the link to the recording in the google doc and hopefully into sched

04:22:17
LINK TO NETPYNE SLIDES: bit.ly/cns20-netpyne

04:22:50
LINK TO NETPYNE SLIDES: http://bit.ly/cns20-netpyne

04:23:11
LINK TO ONLINE NETPYNE GUI: www.netpyne.org/gui

04:23:25
LINK TO ONLINE NETPYNE GUI: http://netpyne.org/gui

04:27:19
@Rebekah We will post a link to the videos on the tutorial website: https://sites.google.com/neurosim.downstate.edu/cns2020-tutorial/home#h.x13r18wekjra

04:32:09
These two code do the same thing?

04:32:20
The information contains appears to be different.

04:33:19
yes

04:33:22
yes

04:33:38
yes

04:33:39
yes

04:33:39
yes

04:33:40
yes

04:33:42
yes

04:35:07
Let us know in chat if you have trouble getting the gun to run in your browser.

04:35:13
gui

04:35:49
Are we going to have access to this gui after the workshop?

04:35:53
all good

04:36:08
yes we have

04:36:13
access

04:36:21
yes, netpyne and the gui is available to everyone already

04:36:50
thanks a lot!

04:43:44
WHy only prototyping and beginners?

04:44:06
awsome

04:46:04
@Wouter The GUI is a great place to start, but it doesn’t have all of NetPyNE’s functionality. More advanced users tend to run everything from the command line.

04:46:39
We are constantly expanding the GUI functionality, but it will always lag behind the codebase.

04:46:59
but note that everything that’s done in NetPyNE’s GUI (or NEURON’s GUI) can be exported to code so that you can always start in the GUI and switch to code

04:48:31
but can we have access to the Neuron objects when we export? For e.g., if I want to code a more sophisticated rule

04:50:02
yes, you can get access to the underlying NEURON objects

04:53:00
https://www.biorxiv.org/content/10.1101/201707v4

04:54:37
https://arxiv.org/abs/2005.03764

04:55:52
bit.ly/CNS20-netpyne

04:55:55
what are some advantages of NetPyNe over BMTK? better visualization tools?

04:57:05
perhaps better in some respects; also more scales -- down to reaction-diffusion

04:58:58
I don’t see the arrow. Does it work on firefox?

04:59:33
should work on firefox but perhaps try chrome/chromium

05:00:27
Sorry could you repeat how to create a cell? Mine stops working

05:00:52
click on cell type

05:01:05
Netpyne vs bmtk - there are many similarities and both have pros and cons… some advantages of netpyne are: full declarative language, molecular scale (rxd), built-in parameter optimization methods, and the Graphical User Interface (GUI)

05:02:08
are they randomly sized?

05:02:19
automatically inside a population

05:02:38
all the neurons will be same size

05:02:56
population size will be defined by you as well

05:02:58
ok thx

05:03:07
if anyone missed -- http://netpyne.org/gui to bring up the gui

05:03:23
And if you miss a step you can always check the slides, which contain step-by-step instructions - http://bit.ly/cns20-netpyne

05:04:45
what is the effect of weight ?

05:04:53
If I want to add some inhomogeneity to the synaptic weights, what should I do?

05:04:54
strenght of the synapse

05:05:31
Weight = synaptic conductance?

05:05:47
will scale the synaptic conductance in general

05:05:54
can custom models of synapses be integrated?

05:05:58
yes

05:06:23
most syn models will be written in NMODL (.mod) and would be included during nrnivmodl compilation

05:07:36
it’s too quick ...

05:07:56
need to catch up

05:08:34
When I press enter at this location

05:08:51
red roundish box with dend is created

05:09:17
can I get access to the tutorial model so I can just load it? I missed a lot in the beginning ...

05:09:18
press enter?

05:09:28
inhomogeneity in syn weights - you can use custom math expressions, see: http://www.netpyne.org/reference.html#function-string

05:10:25
Mainak - you can load the tutorial from the Tutorials menu -> Tutorial 1 (to avoid issues first do File -> New -> Blank)

05:10:27
access to the tutorial from Tutorial list at top

05:10:39
still on Tut 1

05:11:17
Thank you salvador : )

05:12:16
v_soma : { sec: soma, loc: 0.5, var: v}

05:12:52
v_dend : { sec: dend, loc: 0.5, var: v}

05:13:07
v_dend : { sec: dend, loc: 1.0, var: v}

05:14:04
Error while instantiating the NetPyNE model

05:14:10
Any way to find out what I did wrong?

05:14:55
What are the debugging options?

05:15:27
We are working on providing feedback for errors; probably the best for now is click File->New->Blank and then load Tutorials -> Tutorial 1 from the menu

05:15:34
not yet a lot of error msgs .... working on that

05:16:10
you can try again later using the step slides or the tutorial recording

05:16:37
I can’t get Post-Synaptic Cells to be E Populatiion

05:16:52
How do I select E

05:17:24
The little arrow, and then click on E

05:17:30
Thanks, this was great!

05:17:49
it's AWESOME!

05:17:58
Time line when the errors wlll be informative for users trying to debug their work?

05:18:29
Yes, thats the idea

05:18:41
thanks Sid and rozita

05:19:43
time line -- 3-6 mon i'd say

05:19:55
what do the 3D points represent? many more than the beginning & end of a section

05:20:24
3Dpts give locations as sections curve

05:20:29
so many points to a section

05:20:44
and segments (cf nseg) are yet another measure along the section

05:20:45
the 3D points are the kind of data you get from NeuroMorpho.Org

05:21:31
so end up with 3 measures actually 0-1 along sec, loc of each seg, 3Dpts -- 3Dpts have no effect electrically but will make a difference in terms of molec diffusion

05:23:37
Could you explain what netstim means? Thank you

05:23:47
network stimulus

05:23:56
so like… here’s an artificial synaptic input

05:23:57
is there some way to output the system of equations that are actually being simulated -- in case we want to check something

05:24:09
Netstim is an artificial spike generator that you can connect to cells

05:24:22
from outside of the modeled cell… you could have it generate according to a poisson train, or regular, or..

05:24:39
To every cell? Thank you Robert and salvador

05:24:57
you can feed input into your model however you want

05:25:20
yugarshi - yes, you can generate the python code from the GUI model

05:25:34
ok thx!

05:25:44
Is this connectivity generated on the backend? Or on the frontend?

05:26:12
When hitting generate network does this result in resource utilization on a potential HPC system?

05:26:12
backend

05:26:28
Yes

05:27:11
Any experience with punching firewall holes at HPC centers?

05:28:12
'type arbitrary python code' and launch on a HPC node?

05:31:40
You could use the GUI to submit a job on a HPC, but the GUI does not have to run in a HPC.

05:35:19
Wouter -- but generally if you have access to an HPC and run python you can now run arbitrary code, right? so always a risk once someone can login; but you're saying that this will be used by students who normally wouln't have login

05:35:50
Is the spacing scaled for mouse, what about larger animals like monkey etc?

05:37:16
Correct, but this would be a logged in user. That accepted the usage contract. Has handed in his personal details.A webtool that is open can not be checked this way.

05:37:45
fair

05:38:02
There are solutions: special accounts, but it shifts the responcibility to the front-end application.

05:38:08
can rescale spacing as needed for species

05:38:19
thanks!

05:38:36
And I would not take responcibility for arbitrary python code.

05:39:27
Obviously you can still get around things, but the obviously security holes should be plugged.

05:40:46
@Wouter - when netpyne will be integrated to HPC resource, I assume netpyne will be behind some authentication mechanism. Same as HBP collab discussions in the past.

05:41:16
can you explain this figure a bit? What are we seeing? The wider cylinders are the soma?

05:42:13
current fig cylinder is a pump

05:42:17
is there a verbose mode so that a user knows that something is actually running and not hanging?

05:42:21
SERCA pump from ER to cytoplasm

05:42:37
sorry I meant the previous figure in the GUI, it’s not on screen anymore ...

05:42:43
never mind

05:42:55
should be a little spinning thing but yeah hanging can be a problem

05:43:07
we should add some time updates

05:43:49
@pramod. Both is possible: public access or with login.IMHO this tool is fancy and should be available for the general public.

05:44:19
When you run a new simulation with a different set of parameters, is there a way of storing the previous set of simulations for “easier” comparison?

05:44:59
can store the code to the netpyne files (simConfig.py netParam.py)

05:45:10
can output the results to files in pkl or json etc

05:45:19
since connections are random -- can the same network be run multiple times so one can collect statistics on the same network run multiple times

05:45:29
yes

05:45:34
It turned blank

05:45:42
Given that this is tool for teaching / prototyping. A third deployment option would be on the FENIX resources: These are fully public facing, not directly connected to the HPC data stores, You own the VM and data space that can be accessed. Any 'problems' would be your own.

05:45:52
we generally run 5 random wirings and 5 random input vectors (for driven sims)

05:45:54
If it turns blank, refreshing usually works.

05:46:00
ok

05:46:30
I added a Feedback section to the Google Doc (https://docs.google.com/document/d/1GCv6JVFX9Zm0wIAcsKaRFlppx9KMPhN7-1p25NqRdx8/edit#)

05:46:32
Still blank refreshed a couple times

05:46:44
same for me just a blank black screen

05:46:58
We would love feedback and suggestions for improvement.

05:47:05
usually reload works but worst case start again

05:47:15
feedback -- don't crash :)

05:47:27
:)

05:47:54
Visualization is done on the frontend?

05:48:07
Backend also

05:48:09
Analysis also?

05:48:11
i believe that that's all running backend?

05:48:30
most is backend -- calc backend -- facu?

05:48:37
What is send? 2d pixels are preprocessed d3js objects?

05:48:42
Yes, all backend.

05:49:06
Is that possible to simulate different brain states such as slow wave sleep using the GUI? Or will that be possibly carried out using code?

05:49:22
this is js mystery to me -- not sure how js represents stuff - this html5 i think?

05:49:23
can I run the GUI locally on my computer?

05:49:35
Still blank

05:49:40
:(

05:49:57
i think would be good idea to be able to get on individual computer or hpc but has proved hard to get a decent install script

05:49:59
Try opening an incognito browser and going to netpyne.org/gui again.

05:50:04
We have three js for 3d and iframe for the plots

05:50:06
same. I've restarted browser, itll say initializing Neypyne then just nothing

05:50:08
ok

05:50:15
brain states depend on changes in conductances so could do that all in GUI

05:50:39
/cough containers /cough

05:50:41
We’ve never had this many people using the GUI simultaneously. Sorry for any issues!

05:50:56
yes docker -- that's doable

05:51:05
singularity

05:51:14
containers make a contained version work, but then it’s not integrated with your system

05:51:14
incognito seems to be working, thanks!

05:51:29
containers are not a good solution for software packages

05:51:43
singularity is the HPC version that does tie in with the system

05:51:47
Thank yuo

05:51:52
you

05:51:53
Thanks Alison, yeah, it froze for me on normal, but runs in incognito.

05:51:57
containers -- what's disadvantages?

05:52:04
they’er contained

05:52:04
yep

05:52:07
versioning

05:52:19
magic

05:52:26
Does the NetPyNE GUI work as well for the regular NEURON code written in Python?

05:52:28
the underlying software is contained but source files can come in and out

05:52:33
storage of objects

05:52:35
if I have two softwares using Neuron, they won’t use the same Neuron because they’re in different containers

05:52:38
too much memory

05:52:51
ic

05:53:03
no

05:53:09
avoid too many dependencies

05:53:15
y

05:53:33
"NetPyNE GUI work as well for the regular NEURON code written in Python? " -- will not extract things fully

05:53:56
for that can use ModelView in the old interviews GUI

05:54:23
(or ModelDB’s ModelView)

05:54:30
better

05:56:49
In defining the mechanism under cell section, are these predefined and only the parameters are allowed to be changed?

05:57:23
can you make an external NetConn input in NetPyNE, using make_event() method?

05:57:26
which mechanism? -- all can be selected for insertion

05:57:43
external -- use NetStim

05:58:37
You can load your own MOD files into the application

06:01:16
Got it

06:03:45
All good for me

06:03:51
Works fine

06:04:12
I get:

06:04:14
There was an exception in plotRaster():matplotlib is required for plotting when the default backend "matplotlib" is selected.(<class 'ImportError'>, ImportError('matplotlib is required for plotting when the default backend "matplotlib" is selected.',), <traceback object at 0x7f3c7fddef08>)Plotting spike histogram...

06:04:21
me too

06:04:43
me too

06:05:16
Raster plot gave an error but histogram and spectral was ok

06:05:22
Plotting raster...There was an exception in plotRaster():matplotlib is required for plotting when the default backend "matplotlib" is selected.

06:06:12
It says error for downloading netpyne and neuron

06:06:20
same for the raster plot for me

06:07:20
it worked after running everything

06:07:30
after restart

06:07:44
here was an exception in plotRaster():matplotlib is required for plotting when the default backend "matplotlib" is selected.(<class 'ImportError'>, ImportError('matplotlib is required for plotting when the default backend "matplotlib" is selected.',), <traceback object at 0x7f63400ffe48>)Plotting spike histogram...

06:08:37
I don’t know if it made a difference but it ran OK starting with an incognito browser and then signed into a google account

06:08:56
yeah

06:09:28
Still got error after running in order, will retry

06:09:46
could you once more share a link to the colab?

06:09:59
try restart and run all

06:11:07
Thanks Shivangi- worked for me

06:11:18
Click ‘Runtime’ in the CoLab File Menu and then click ‘Restart and run all’

06:11:29
Thanks Shivagi.

06:14:22
Thanks, that worked for me now.

06:17:47
What is sync? How is it being measured?

06:18:06
I mean understand it as the strength of synchrony, but I mean how is it measured?

06:19:03
How can I load a model downloaded from ModelDB to NetPyNE?

06:19:18
@Maliha see here: http://www.scholarpedia.org/article/Neuronal_synchrony_measures

06:19:37
Thanks, Joe!

06:21:47
@Rozita We are collaborating with OSB (Open Source Brain) to make it easier to get models into NetPyNE.

06:22:19
in general a NEURON sim eg in modeldb will need to be ported to netpyne

06:23:11
That would be so great! thanks

06:23:20
@Rozita: File -> Workspace -> Upload

06:23:35
can you connect morphologically detailed units with gap junctions, specify their location and so on?

06:23:53
yes

06:24:13
great, thanks!

06:24:29
Can hoc and mod files which were used with NEURON be imported directly ?

06:24:47
hoc files for morph and all mod files yes

06:25:10
@Natalie: see here: https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut_gap.py

06:25:14
generic hoc code with eg loops creating cells can be imported but won't be in netpyne -- can't be parsed

06:27:21
@Joe for tut_gap.py we need development branch?

06:28:28
It indicates that it plotted but there are no graphics?

06:28:30
this transfer works because we are starting wiht netpyne code not with arbitrary python code to define a network

06:28:53
you have to page down to see the graphics

06:29:06
but better yet is to do this copying salva is now doing

06:29:13
netpyne_geppetto.netParams = netParamsnetpyne_geppetto.simConfig = simConfig

06:29:17
so can see everything in the netpyne-GUI graphics

06:29:19
@sidimtra Nope, it’s available in Master and also, we just released a new version of NetPyNE, so the pip3 install netpyne is identical to development.

06:29:56
Could someone past the code

06:30:27
@Joe Thanks!

06:34:16
joe where is all this code? - pointer?

06:34:52
excellent, thx

06:34:53
!

06:35:15
Maybe helpful to have a list of params that were modified during the demo

06:36:09
thank you!

06:36:12
Thanks!

06:36:17
Thank you

06:36:23
This has been wonderful. Thank you!

06:36:24
Thank you

06:36:26
Thanks, great tutorial!

06:36:26
thank you

06:36:29
Thanks Salva

06:36:32
This was fantastic thank you so much!!!

06:36:32
@sidmitra The params list is at the end of code on collab

06:36:32
Thanks a lot!

06:36:38
Thank you. Very nice

06:36:40
Great job Salva!

06:36:41
Thank you very much.

06:36:43
Thanksa lot!

06:36:44
great tutorial, thanks a lot!!

06:36:47
Thank you

06:36:50
great tutorial! thank you

06:36:52
thank you very much

06:36:52
thank you so much!

06:36:52
thanks - this was great!

06:37:19
thank you!!!

06:37:20
thank you so much!

06:37:24
fantastic workshop! thank you!!

06:38:11
Thank you very much for a through tutorial. Just a quick q: how do you compare netpyne for net sims with Brian or NEST?

06:38:14
You’re still broadcasting

06:38:21
Thanks so much everyone, great session :)

06:39:14
Just wanted to ask: will the link for the recording be provided if someone missed a part of the workshop?

06:39:31
Link will be posted to the tutorial website

06:39:42
Thanks!

06:39:57
https://sites.google.com/neurosim.downstate.edu/cns2020-tutorial/home

06:40:42
Yes the link fro the recording will be available on Sched and the netpyne web

06:44:24
Thank you again. See you at the next dev meeting

06:47:50
Thanks and bye

06:47:59
thanks