Search found 5753 matches

by ted
Mon Jul 13, 2020 10:35 pm
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 107

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

now isst is set to the flux of sst . . . writing ssti in this block did not change the above result. Another couple of misunderstandings appear to have emerged. First, the trivial one. NMODL expects currents to be in units of absolute current (nA) or current density (mA/cm2), depending on whether t...
by ted
Mon Jul 13, 2020 2:55 pm
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 107

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

I did not know that a current for an ion with valence 0 would affect the charge balance equation. I don't know for sure, would have to run a test to verify, but it seems reasonable. As far as I know, valence is used only by NEURON's computational engine when the ion_style settings tell NEURON to ca...
by ted
Mon Jul 13, 2020 1:10 am
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 107

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

Should I repost Not at all. They routinely monitor this part of the Forum. I was just declaring the limited scope of my own comments. I don't see a reason for inconsistencies outside of a typo I have just seen too much user-written NMODL code. One of the advantages of the rxd module is the convenie...
by ted
Sun Jul 12, 2020 2:46 pm
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 107

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

adamjhn or ramcdougal will have to answer your rxd-specific questions. I have some questions about the NMODL code: All those variable names and parameter values, but no units. You're sure there are no units inconsistencies? that no scale factors are necessary? Why USEION sst READ ssti, ssto WRITE is...
by ted
Fri Jul 10, 2020 10:58 pm
Forum: NEURON + Python
Topic: Best practice to run hundreds of simulations / remove all objects between runs
Replies: 6
Views: 149

Re: Best practice to run hundreds of simulations / remove all objects between runs

Some of the posts in those previous threads illustrate that it is always possible to write complex code that has unintended, undesirable side effects. In the past two days I used Python to work with two different implementations of simulation experiments wrapped in class definitions. One implementat...
by ted
Thu Jul 09, 2020 11:24 pm
Forum: NEURON + Python
Topic: Best practice to run hundreds of simulations / remove all objects between runs
Replies: 6
Views: 149

Re: Best practice to run hundreds of simulations / remove all objects between runs

Ah, my mistake. What worked from hoc may need modification to work from Python. For a very pertinent discussion on the forum, see this thread Running multiple simulations in one process https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=3213 Sure enough, h.delete_section() is discussed in the Pro...
by ted
Thu Jul 09, 2020 9:56 pm
Forum: Optimization
Topic: MRF on HH voltage curve
Replies: 3
Views: 68

Re: MRF on HH voltage curve

That's all the MultiRunFItter tutorials of which I am aware. The two ModelDB entries are examples of practical application of the MRF to research problems (specifically, fitting a model to experimental results recorded from a spiking neuron). Maybe you'd be interested in BluePyOpt https://www.fronti...
by ted
Thu Jul 09, 2020 2:35 pm
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 4
Views: 145

Re: Does the usage of the Shape may affect mV readouts?

Did you resolve the problem yourself, or do you still have a question?
by ted
Thu Jul 09, 2020 2:33 pm
Forum: NEURON + Python
Topic: Best practice to run hundreds of simulations / remove all objects between runs
Replies: 6
Views: 149

Re: Best practice to run hundreds of simulations / remove all objects between runs

After you have debugged your model, put all necessary statements (including model setup, instrumentation, simulation flow control, analysis, and i/o) inside a Python class definition. Assuming you called this class ModelInABox you can get a new instance of this class any time you want: new_instance ...
by ted
Thu Jul 09, 2020 2:20 pm
Forum: Optimization
Topic: MRF on HH voltage curve
Replies: 3
Views: 68

Re: MRF on HH voltage curve

Is it possible to use the MRF to fit the desired voltage curve of the standard HH neuron?
Yes. You might find these ModelDB entries interesting:
modeldb.yale.edu/3342
modeldb.yale.edu/3793
by ted
Sun Jul 05, 2020 11:23 am
Forum: The GUI
Topic: NetGUI weights
Replies: 2
Views: 91

Re: NetGUI weights

They are the weights associated with the NetCons that connect a presynaptic spike source to a postsynaptic target (e.g. event-driven synaptic mechanism). At a minimum, read about the NetCon class in the Programmer's Reference. Would be a good idea to also read chapter 10 of The NEURON Book and/or Hi...
by ted
Fri Jul 03, 2020 10:45 am
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 4
Views: 145

Re: Does the usage of the Shape may affect mV readouts?

See my message from June 29.
by ted
Tue Jun 30, 2020 10:44 am
Forum: NEURON hacks
Topic: Using NetCon where voltage is not the threshold variable
Replies: 3
Views: 244

Re: Using NetCon where voltage is not the threshold variable

If your conceptual model of the extracellular space that contains the chemical signals involved just a few compartments, then NMODL might have sufficed. However, if you prefer a continuum, then rxd is probably the best choice. If you could, please open a new discussion thread in the Forum's Reaction...
by ted
Mon Jun 29, 2020 12:57 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Arbitrary waveform
Replies: 1
Views: 126

Re: Arbitrary waveform

I used NMODL to generate the sine and biphasic square wave stimulus waveforms for three reasons: 1. properly written NMODL code "plays well" with adaptive integration 2. by exposing parameters but hiding implementational details, an NMODL-specified waveform generator offers the greatest convenience ...
by ted
Mon Jun 29, 2020 12:42 pm
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 4
Views: 145

Re: Does the usage of the Shape may affect mV readouts?

Before commenting I will need to see this for myself. The model authors describe more than one way to launch the model. Exactly what did you do?