## Search found 6101 matches

Fri Feb 03, 2023 12:15 am
Forum: NEURON + Python
Topic: Steady state init with voltage VS with SaveState
Replies: 1
Views: 50

### Re: Steady state init with voltage VS with SaveState

Compute steady state of the cell given channel mechanismes ( voltage of all compartments do not vary more than 1e-6 mV from previous step) 1. Experimentalists typically wait until v near the spike trigger zone is flat for an amount of time on the order of at least several seconds if not minutes. An...
Tue Jan 31, 2023 2:26 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 41
Views: 1091

### Re: pyramidal spine-neck EPSPs

In modeldb.science I found several calcium models written for NEURON Excellent. "Spine neck plasticity controls postsynaptic calcium signals" (Grunditz et al. 2008) That's an interesting paper. at the c> typed cd then nrnivmodl and it worked It's great when things work the way they should...
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: 48

### 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
Fri Jan 27, 2023 12:43 pm
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 13
Views: 249

### 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...
Fri Jan 27, 2023 11:34 am
Forum: NEURON + Python
Topic: Nstack - stack too deep in python
Replies: 2
Views: 222

### Re: Nstack - stack too deep in python

Thanks for following up with your solution.
Wed Jan 25, 2023 1:11 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 41
Views: 1091

### 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...
Tue Jan 24, 2023 2:23 pm
Forum: NEURON + Python
Topic: Stimulating a Cell
Replies: 7
Views: 248

### 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...
Tue Jan 24, 2023 1:35 pm
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 13
Views: 249

### 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.
Tue Jan 24, 2023 1:31 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 41
Views: 1091

### 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...
Fri Jan 20, 2023 1:01 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 41
Views: 1091

### 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 ...
Fri Jan 20, 2023 12:24 am
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 13
Views: 249

### 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...
Mon Jan 16, 2023 4:06 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 41
Views: 1091

### 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. ...
Mon Jan 16, 2023 3:52 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 41
Views: 1091

### 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...
Mon Jan 16, 2023 1:21 pm
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 13
Views: 249

### 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...
Fri Jan 13, 2023 2:03 pm
Forum: NEURON + Python
Topic: Stimulating a Cell
Replies: 7
Views: 248

### 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.