Search found 6062 matches

by ted
Wed Dec 07, 2022 12:02 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to get total receptor current
Replies: 1
Views: 24

Re: How to get total receptor current

It's not a stupid question. It is directly related to one of the most common questions in computer programming: what is the name of some important variable? I have implemented 1000 nAChR You may know what you mean by "nAChR" but nobody else does. To say "I have a model of X" says...
by ted
Mon Dec 05, 2022 12:23 pm
Forum: NEURON + Python
Topic: Switching L2/3 morphology in model but preserving intrinsic and synaptic properties.
Replies: 2
Views: 36

Re: Switching L2/3 morphology in model but preserving intrinsic and synaptic properties.

Is there an automatic way I can scale the synaptic inputs and intrinsic property distributions to the new morphology Nothing is automatic. You have to understand the procedures/functions that the original authors used to govern distribution of channels, synapses, etc., and decide what changes are n...
by ted
Mon Dec 05, 2022 12:12 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 6
Views: 81

Re: pyramidal spine-neck EPSPs

Not to open a different discussion, but in the experiments by Cornejo et al. 2022, why were "spine-only events" observed only as spontaneous events? What accounts for the failure to elicit them by photostimulation? Maybe I missed this, but did they find a subset of spines in which both spi...
by ted
Mon Dec 05, 2022 11:10 am
Forum: NEURON + Python
Topic: how to add a current clamp in Python?
Replies: 1
Views: 31

Re: how to add a current clamp in Python?

The Vector class's play() method can be used to force the current delivered by an IClamp to follow an arbitrary waveform. However, if the waveform can be described by a function or algorithm, it might be easier to implement the function or algorithm in NMODL. The resulting point process would also b...
by ted
Wed Nov 30, 2022 1:43 pm
Forum: Optimization
Topic: how to address errno
Replies: 2
Views: 46

Re: how to address errno

The first thing to check is the NMODL source code. "For what?" you might ask. The list of possible problems includes typographical errors (e.g. using a minus sign instead of a plus), failure to include scale factors needed to resolve inconsistencies of units, algebraic formulas that are wr...
by ted
Wed Nov 16, 2022 1:34 am
Forum: NEURON + Python
Topic: recording delivered pulses using pulsedistrib.zip
Replies: 3
Views: 73

Re: recording delivered pulses using pulsedistrib.zip

First I would like to say that the syntax This works: from neuron import h soma = h.Section(name='soma') pstim = h.Ipulse2(soma(0.5)) "h.ipulse2(bs.soma(0.5))" gives error "hoc object doesn't have attribute ipulse2" which tells me that I am using the wrong syntax. True. The clas...
by ted
Tue Nov 15, 2022 11:46 am
Forum: NEURON + Python
Topic: recording delivered pulses using pulsedistrib.zip
Replies: 3
Views: 73

Re: recording delivered pulses using pulsedistrib.zip

Good questions. Before addressing them, I should mention that 1. you're asking about mechanisms that deliver a series of one or more current pulses at regular intervals 2. the source code for these mechanisms is in https://www.neuron.yale.edu/ftp/ted/neuron/pulsedistrib.zip 3. these mechanisms diffe...
by ted
Thu Nov 10, 2022 1:51 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: modlunit Conversion Factor
Replies: 2
Views: 107

Re: modlunit Conversion Factor

Rather than writing something from scratch, it is generally quicker and easier to proceed by modifying existing NMODL code that works properly, does something similar to what one wants, and follows best practices. Among the files included with NEURON's source code (downloadable as a zip file from ht...
by ted
Tue Nov 08, 2022 3:44 pm
Forum: NEURON + Python
Topic: Extracellular Stimuli with Python + Vector Play
Replies: 2
Views: 1194

Re: Extracellular Stimuli with Python + Vector Play

I suspect that each pass through the loop for seg in axon: potential = . . . discards the vector that was created on the previous pass, thus breaking vector play into the previous seg. See what happens if you change the loop to ffvecs = [] # a list to hold the forcing function vectors for seg in axo...
by ted
Tue Nov 08, 2022 3:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: modlunit Conversion Factor
Replies: 2
Views: 107

Re: modlunit Conversion Factor

This is a tough one--raises a lot of questions for me, even before we get to your question. Neiman et al. 2011 doesn't ring a bell. PubMed search wasn't helpful. Maybe something in that article would explain why it was necessary to express K current in terms of the GHK current equation, and why P is...
by ted
Wed Nov 02, 2022 3:28 pm
Forum: NEURON + Python
Topic: Depolarization step during voltage clamp
Replies: 4
Views: 90

Re: Depolarization step during voltage clamp

Sounds like the SEClamp's series resistance rs is too high for your particular model cell. Looking at the documentation of SEClamp I see that the default value of rs is not mentioned. Not a problem--it's very easy to discover. Start python, then execute the following commands at the python prompt fr...
by ted
Tue Nov 01, 2022 3:48 pm
Forum: NEURON + Python
Topic: Depolarization step during voltage clamp
Replies: 4
Views: 90

Re: Depolarization step during voltage clamp

The first question to ask yourself is: why use an instance of the VClamp class to do this? In the Programmer's Reference, note that VClamp https://nrn.readthedocs.io/en/latest/python/modelspec/programmatic/mechanisms/mech.html#VClamp is described as Two electrode voltage clamp. Last time I saw anyon...
by ted
Fri Oct 28, 2022 11:55 am
Forum: NEURON + Python
Topic: record calcium concentration only from pyramidal cells
Replies: 2
Views: 141

Re: record calcium concentration only from pyramidal cells

If I call"cai" in the mod file that calculates DSI, it appears to me, that I record the net calcium concentration in all cells (not just pyramidal cells) I don't see how this could possibly be a problem. A synaptic mechanism is usually implemented as a point process. A point process is at...
by ted
Tue Oct 25, 2022 12:34 pm
Forum: Other questions
Topic: List of all currents that comprise segment membrane current
Replies: 3
Views: 607

Re: List of all currents that comprise segment membrane current

when we use forward Euler's integration method Then you must be using some other program than NEURON. NEURON doesn't offer the option of forward Euler. NEURON's fixed time step integration methods are limited to implicit Euler (which is the default method and has first order numerical error) and tw...
by ted
Fri Sep 30, 2022 4:13 am
Forum: NEURON + Python
Topic: Insert an ion channel written in a .mod file
Replies: 8
Views: 820

Re: Insert an ion channel written in a .mod file

That's because you put the NMODL files in a directory other than the one that contains your hoc and Python files. When NEURON starts, it automatically looks in the current directory for a library of compiled mechanisms; under MSWin, that library is called nrnmech.dll. If that file is in some directo...