Search found 5749 matches

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: 107

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: 107

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: 53

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: 137

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: 107

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: 53

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: 79

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: 137

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: 208

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: 121

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: 137

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?
by ted
Mon Jun 29, 2020 11:51 am
Forum: Hot tips
Topic: NEURONS v is different than mine
Replies: 1
Views: 123

Re: NEURONS v is different than mine

At first I wrote one of the models into a single mod file I don't know anything about your expertise with NEURON or NMODL, but I do know that 1. Most user-written code contains errors, especially NMODL code. 2. All but the most trivial code has bugs. The only question is whether the effect of any p...
by ted
Fri Jun 26, 2020 10:33 am
Forum: NEURON hacks
Topic: Using NetCon where voltage is not the threshold variable
Replies: 3
Views: 208

Re: Using NetCon where voltage is not the threshold variable

The NetCon class is useful for spike-triggered synaptic communication, in which it is often reasonable to assume that presynaptic details can be ignored. Signaling that is continuous in time cannot be properly represented with a NetCon. Continuous transmitter release can be implemented with NMODL's ...
by ted
Tue Jun 23, 2020 4:29 pm
Forum: NEURON + Python
Topic: ampanmda mod file working with AlphaSynapse
Replies: 7
Views: 899

Re: ampanmda mod file working with AlphaSynapse

I would like to have more control over the EPSP shape and parameters, which the NetStim module doesn't offer me. In NEURON, a synaptic mechanism does not perturb membrane potential directly. It generates a current or a current + conductance change, which interacts with the electrical properties of ...
by ted
Mon Jun 22, 2020 11:54 pm
Forum: NEURON + Python
Topic: Error recording channel current by passing string to Vector.record
Replies: 3
Views: 167

Re: Error recording channel current by passing string to Vector.record

The problem is that Vector.record doesn't accept a string as its argument--it wants something that the parser recognizes to be a recordable variable. If you are determined to continue on this path, as an experiment you might see if Vector.record(eval(somestring)) succeeds; if it doesn't, you could t...