Search found 6099 matches

by ted
Mon Jan 30, 2023 10:35 pm
Forum: Employment and educational opportunities
Topic: 2 Assist. Prof. positions at Stanford U Psychiatry Dept
Replies: 0
Views: 4

2 Assist. Prof. positions at Stanford U Psychiatry Dept

The Psychiatry Department at Stanford University School of Medicine announced two research (non-tenure) positions in computational neuroscience at the Assistant Professor level. For more information see https://facultypositions.stanford.edu/c ... job/493518
by ted
Fri Jan 27, 2023 12:43 pm
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 12
Views: 191

Re: how to add a current clamp in Python?

The new code still uses a conditional statement. The INITIAL block sets both i_1 and i_2 to 0, so both of these variables will stay equal to 0 forever. This mechanism will deliver 30 nA for the first 30 ms, after which it will deliver 15 nA forever. That's definitely not what you want. Maybe I don't...
by ted
Fri Jan 27, 2023 11:34 am
Forum: NEURON + Python
Topic: Nstack - stack too deep in python
Replies: 2
Views: 193

Re: Nstack - stack too deep in python

Thanks for following up with your solution.
by ted
Wed Jan 25, 2023 1:11 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 39
Views: 837

Re: pyramidal spine-neck EPSPs

ModelDB login is used only by ModelDB admins, and a small number of people who want to perform administrative tasks on their own particular model entries (most model authors leave those tasks to ModelDB's admins). Login is not needed to browse ModelDB's contents, search for models (by author, keywor...
by ted
Tue Jan 24, 2023 2:23 pm
Forum: NEURON + Python
Topic: Stimulating a Cell
Replies: 7
Views: 195

Re: Stimulating a Cell

I needed (okay, wanted) to implement a version of interp_zyx.hoc and calc_rxc.hoc functions in Python Have you verified that your Python code properly calculates the locations of segment centers? One way to demonstrate this is graphically. For example, treat the x3d data from a real neurite as samp...
by ted
Tue Jan 24, 2023 1:35 pm
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 12
Views: 191

Re: how to add a current clamp in Python?

if I want the current to have two decays
then come up with a set of ODEs or a kinetic scheme that will produce such a time course, and I'll show you how to implement those equations properly in NMODL.
by ted
Tue Jan 24, 2023 1:31 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 39
Views: 837

Re: pyramidal spine-neck EPSPs

measure the ca++ concentration in the spine_neck during synaptic transmissions from the spine_head Then you need an "ion accumulation mechanism" for calcium. The simplest mechanisms consider only transmembrane flux through ion channels, might include buffering (most intracellular Ca is bo...
by ted
Fri Jan 20, 2023 1:01 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 39
Views: 837

Re: pyramidal spine-neck EPSPs

If you want to add the calcium current described by the code in cachan.mod to your model, put a copy of cachan.mod in the same directory as your hoc and ses files and then compile it (at nrn.readthedocs.io click on the item Guides in the left column, and in the page that pops up search for How do I ...
by ted
Fri Jan 20, 2023 12:24 am
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 12
Views: 191

Re: how to add a current clamp in Python?

in this mod file, what should I write in Python code to give a value to weight Nothing. Do not change the NMODL code. The weight associated with an event is specified by the weight parameter of the NetCon that (1) detected the presynaptic spike and (2) delivers the event to the synaptic target mech...
by ted
Mon Jan 16, 2023 4:06 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 39
Views: 837

Re: pyramidal spine-neck EPSPs

While I’m making sure I’m using accurate algorithms for current in the spine_neck, I thought I might play around with creating an electric field from an electrode adjacent to the neck. So I added electrode point processor. Sorry, that's not something that can be used for extracellular stimulation. ...
by ted
Mon Jan 16, 2023 3:52 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 39
Views: 837

Re: pyramidal spine-neck EPSPs

Taking a peek at spine_neck current flow. Only two graphs show the time course of any current: right upper quadrant, which shows the ionic current through the neck's "pas" channels, and left lower quadrant, which shows capacitive current through the neck's membrane capacitance. There is n...
by ted
Mon Jan 16, 2023 1:21 pm
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 12
Views: 191

Re: how to add a current clamp in Python?

it should represent a current that is injected into the cell through an electrode So this really is to be similar to an IClamp. The name I chose for this particular mechanism is ExpIClamp because it delivers a current that decays monoexponentially with time. Its source code is in a file called expi...
by ted
Fri Jan 13, 2023 2:03 pm
Forum: NEURON + Python
Topic: Stimulating a Cell
Replies: 7
Views: 195

Re: Stimulating a Cell

One more comment: the purpose of some of these graphs is to verify that the extracellular stimulus is actually happening, and reaching the external surface of the model cell--and that it makes sense.
by ted
Fri Jan 13, 2023 11:24 am
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 12
Views: 191

Re: how to add a current clamp in Python?

I am still learning how to describe mechanisms with NMODL. Then it will save your time and mine if I just implement something that matches your needs. As bad as most user-written hoc or Python code may be, the sad truth is that most user-written NMODL code is even worse because of NMODL's peculiari...
by ted
Wed Jan 11, 2023 4:00 pm
Forum: NEURON + Python
Topic: Stimulating a Cell
Replies: 7
Views: 195

Re: Stimulating a Cell

A lot of your code is good, but you're having to wrestle with many different, unfamiliar pieces. Also, not all documentation is as clear or complete as it should be. And, unfortunately debugging is complicated by the fact that, while matplotlib + NEURON is a powerful combination, it doesn't enable i...