Search found 5988 matches

by ted
Fri Jul 09, 2021 6:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Strangeness when recording state variable
Replies: 6
Views: 608

Re: Strangeness when recording state variable

Suggestions about your CaDyn... mod file: I don't know how you're initializing cai, but it might make life easier to do the following: In the NEURON block insert RANGE cai0 In the PARAMETER block insert cai0 = 1e-4 (mM) Insert this new block: INITIAL { cai = cai0 } Why? This mechanism is WRITEing ca...
by ted
Fri Jul 09, 2021 6:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Strangeness when recording state variable
Replies: 6
Views: 608

Re: Strangeness when recording state variable

For me objref caivec caivec = new Vector() caivec.record(&soma.cai(0.5)) works just fine using version 8.0a-575-gd9462cc master (d9462cc) 2021-05-27 and 7.7.1-28.... from way back 2019-08-07 (ah those halcyon pre-viral days). That said, under 8.0.... _THIS_ objref tvec tvec = new Vector() tvec.r...
by ted
Thu Jul 08, 2021 10:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Strangeness when recording state variable
Replies: 6
Views: 608

Re: Strangeness when recording state variable

Good question. First, at the oc> prompt verify that the variable exists. print cell.soma.cai(0.5) If that doesn't work, try cell.soma print cai(0.5) Vector record() expects a pointer. Try caivec.record(&cell.soma.cai(0.5)) or cell.soma caivec.record(&cai(0.5)) It's best to not use cnexp for ...
by ted
Wed Jul 07, 2021 12:57 pm
Forum: Anatomically detailed models
Topic: Looking for a model illustrating spike frequency adaptation
Replies: 2
Views: 378

Re: Looking for a model illustrating spike frequency adaptation

Just about any model that involves a noninactivating delayed rectifier will have spike frequency adaptation. Even the Hodgkin-Huxley model does, although HH's adaptation is nearly complete after ~ 5 spikes or so. You might search for adaptation in ModelDB modeldb.yale.edu or Channelpedia channelpedi...
by ted
Wed Jul 07, 2021 10:38 am
Forum: Hot tips
Topic: NEURON's command line options
Replies: 0
Views: 435

NEURON's command line options

Did you know that NEURON has many command line options? To learn more, execute
nrngui -h
or
nrniv -h
by ted
Thu Jul 01, 2021 5:08 pm
Forum: Getting started
Topic: Can "nrniv" or "nrngui" command accept multiple argument?
Replies: 2
Views: 363

Re: Can "nrniv" or "nrngui" command accept multiple argument?

To answer your own question, execute
nrngui -h
or
nrniv -h
by ted
Tue Jun 29, 2021 10:09 am
Forum: NEURON Announcements
Topic: Tutorial on NEURON and NetPyNE at CNS*2021
Replies: 0
Views: 299

Tutorial on NEURON and NetPyNE at CNS*2021

Interested in learning how to build biophysically detailed neuronal models with NEURON and NetPyNE? Join us for a tutorial at CNS*2021 on Saturday, July 3rd starting at 10am EDT: All times EDT (New York time) 10:00 AM Bill Lytton--Overview: implementing the conceptual model 10:30 AM Robert McDougal-...
by ted
Sat Jun 26, 2021 12:13 am
Forum: NEURON + Python
Topic: Using h.APCount with the extracellular mechanism
Replies: 1
Views: 348

Re: Using h.APCount with the extracellular mechanism

You're sure that 1. the axon is excitable and can propagate a spike 2. you're allowing the simulation to run for long enough that a spike has time to propagate from its point of initiation to the location of the APCount ? Here's a couple of questions for you: Do you know what fraction of run time is...
by ted
Fri Jun 18, 2021 10:04 am
Forum: Getting started
Topic: nan in meaured voltage and current
Replies: 3
Views: 1852

Re: nan in meaured voltage and current

The symptom is nonspecific. Diagnosis requires more information than the statement "I'm getting NAN errors"
by ted
Fri Jun 11, 2021 12:30 am
Forum: NEURON hacks
Topic: nrnivmodl translation rules
Replies: 5
Views: 696

Re: nrnivmodl translation rules

Well, you can see the c code that is generated, so have at it.
by ted
Fri Jun 11, 2021 12:28 am
Forum: Suggestions and Feedback
Topic: Repeated/Wrong Text in NEURON extension to NMODL Doumentation
Replies: 1
Views: 605

Re: Repeated/Wrong Text in NEURON extension to NMODL Doumentation

That's a really old document that seems to have been unchanged for a long time--I have a copy of it from 2011, and it was old then. The error you note was present even in 2011. The text is somewhat agrammatical, and it doesn't have anything to do with VALENCE or "Point_Process" (which, by ...
by ted
Thu Jun 10, 2021 10:03 am
Forum: NEURON hacks
Topic: nrnivmodl translation rules
Replies: 5
Views: 696

Re: nrnivmodl translation rules

those translated C codes still look to me not human readable in my humble opinion. Your humble opinion is mostly correct. Those c files are computer generated, and they're not intended to be human readable. Bits and pieces of them can be understood for very specific purposes, if and when absolutely...
by ted
Thu Jun 10, 2021 9:40 am
Forum: NEURON + Python
Topic: hh.mod + Python + membrane potential at several points of the soma
Replies: 5
Views: 972

Re: hh.mod + Python + membrane potential at several points of the soma

Here https://neuron.yale.edu/neuron/publications/expanding-neurons-repertoire-mechanisms-nmodl you will find a link to a much expanded preprint of a paper that explains how NMODL is used to implement ion channels, transport mechanisms (pumps), and accumulation and diffusion of solutes. Very useful i...
by ted
Mon Jun 07, 2021 10:33 am
Forum: NEURON hacks
Topic: nrnivmodl translation rules
Replies: 5
Views: 696

Re: nrnivmodl translation rules

Are you just trying to figure out how to write NMODL code that does something useful, or are you actually interested in the process that translates NMODL statements into C code?
by ted
Mon Jun 07, 2021 10:26 am
Forum: NEURON hacks
Topic: addng a parameter to mod file
Replies: 1
Views: 832

Re: addng a parameter to mod file

the kitchens of the channel You mean the kinetics. Etymologies: kitchen https://www.etymonline.com/word/kitchen kinetic https://www.etymonline.com/search?q=kinetic I want to add a parameter to the mtau, so it will be mtau*p It looks like you are dealing with a density mechanism (its NMODL block wil...