Search found 5936 matches

by ted
Thu Jul 22, 2021 1:41 pm
Forum: NEURON + Python
Topic: Exporting .ses from Linear Circuit Builder
Replies: 1
Views: 49

Re: Exporting .ses from Linear Circuit Builder

ckelley was actually trying to use the Linear Circuit Builder to export a template (class definition in hoc) for a class that, when instantiated, would add to NEURON the equations that describe a circuit. That's different from saving a session file--a session file contains code that recreates one or...
by ted
Sat Jul 17, 2021 3:29 pm
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 5
Views: 151

Re: Pass ._ref_concentration to pc.source_var()?

Ma et al. 2013 Presumably you're referring to Tang et al. 2013 in PLoS One, DOI: 10.1371/journal.pone.0080324. Since you're already using rxd, it will be most natural to follow my second suggestion rxd-implemented mechanism in the astrocyte(s) that generates an efflux of the released substance and ...
by ted
Sat Jul 17, 2021 12:56 am
Forum: Other questions
Topic: calculate IPSP by IPSC
Replies: 3
Views: 99

Re: calculate IPSP by IPSC

Something to think about before you go any further: D_Cl is 2 um2/ms. That means radial concentration gradients vanish rapidly in neurites with diameters on the order of 5 um or smaller. Much faster than the time course of GABA-A synaptic conductance change or transmembrane current. This means chlor...
by ted
Fri Jul 16, 2021 11:40 pm
Forum: Other questions
Topic: Rectifying gap junctions
Replies: 1
Views: 39

Re: Rectifying gap junctions

Yes.
by ted
Fri Jul 16, 2021 1:16 pm
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 5
Views: 151

Re: Pass ._ref_concentration to pc.source_var()?

What are you trying to represent? Calcium-dependent release of neurotransmitters or other substances from astrocytes? Effects on neighboring neurons could be accomplished with a POINTER in an NMODL file for a density or point process mechanism in the affected neuron sections. Another way would be to...
by ted
Fri Jul 16, 2021 10:59 am
Forum: Other questions
Topic: calculate IPSP by IPSC
Replies: 3
Views: 99

Re: calculate IPSP by IPSC

It's feasible but if you want more specific help, you'll need to provide some information about the model that you currently have. Is it a conceptual model (hypothesis) or have you actually implemented a computational model? If it is a computational model, what is your implementation (source code) o...
by ted
Tue Jul 13, 2021 3:18 pm
Forum: NEURON Announcements
Topic: 2021 NEURON Online Course
Replies: 4
Views: 1138

Re: 2021 NEURON Online Course

There are some issues WRT file names that remain to be resolved.
by ted
Sat Jul 10, 2021 1:11 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Strangeness when recording state variable
Replies: 6
Views: 106

Re: Strangeness when recording state variable

under 8.0.... _THIS_ objref tvec tvec = new Vector() tvec.record(&t) doesn't work. Well, that's strange. I tried to reproduce this error message, but couldn't, perhaps because I didn't save the version of my model implementation that generated the messge. I thought I had saved it, but apparentl...
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: 106

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: 106

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: 106

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: 65

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: 41

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: 61

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: 44

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-...