Search found 5602 matches

by ted
Sat Sep 07, 2019 3:33 pm
Forum: Parallel NEURON
Topic: Is it possible to associate multiple gids with the same segment?
Replies: 1
Views: 239

Re: Is it possible to associate multiple gids with the same segment?

Yes, but why bother? Assuming that your conceptual model of spike-triggered synaptic transmission is * transmission is triggered when a presynaptic variable crosses a user-specified threshold * the presynaptic variable is the same for all postsynaptic targets of axons that arise from the presynaptic...
by ted
Sat Sep 07, 2019 12:09 pm
Forum: NEURON + Python
Topic: TypeError: sec is not a Section"
Replies: 3
Views: 352

Re: TypeError: sec is not a Section"

You got it. This would work too
print(cell.soma[0])
stim = h.IClamp(0.5, sec=cell.soma[0])
by ted
Sat Sep 07, 2019 12:07 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mknrndll fils with undefined reference
Replies: 2
Views: 663

Re: mknrndll fils with undefined reference

Compilation of NMODL files produces .o and .c files that persist but are not required during program execution. Why? If you decide to add a new NMODL file, or revise an existing NMODL file, there's no need to recompile all the other files. If you update NEURON, there's no guarantee that the old .o f...
by ted
Thu Sep 05, 2019 1:00 pm
Forum: NEURON + Python
Topic: TypeError: sec is not a Section"
Replies: 3
Views: 352

Re: TypeError: sec is not a Section"

Before we even get started, get rid of the import neuron statement at the top of try.pi. It's not necessary, and conceivably could cause problems. If I run try.py I get the error: "stim = h.IClamp(0.5, sec=soma_py TypeError: sec is not a Section" True, and for good reason. try.py contains no stateme...
by ted
Thu Sep 05, 2019 2:26 am
Forum: NEURON Announcements
Topic: Big models and big data workshop at SFN 2019
Replies: 0
Views: 858

Big models and big data workshop at SFN 2019

NSG and HPAC – Large Scale Simulations and Data Processing A workshop on big models and big data in neuroscience, Saturday, Oct. 19, 2019 from 8:30 AM to 12:30 PM at a downtown Chicago location. Summary This workshop is intended for neuroscientists who need to use high performance computing (HPC) r...
by ted
Tue Sep 03, 2019 1:53 pm
Forum: NEURON + Python
Topic: Save model's biophysics and morphology programmatically to .hoc
Replies: 3
Views: 306

Re: Save model's biophysics and morphology programmatically to .hoc

You can use the GUI's ModelView tool to export a NeuroML specification of the model cell. This is probably doable via hoc statements. I'm not sure how compatible NEURON's current NeuroML ouput is with the current NeuroML specification. Depending on what your simplification algorithm actually does, t...
by ted
Thu Aug 29, 2019 11:33 am
Forum: Other questions
Topic: debugging/profiling NEURON execution
Replies: 3
Views: 388

Re: debugging/profiling NEURON execution

NEURON's standard run system is discussed in some detail in chapter 7 of The NEURON Book. Chapter 8 addresses simulation initialization. If you don't have the book, see these preprints:
https://www.neuron.yale.edu/ftp/ted/book/chap7.pdf
and
https://www.neuron.yale.edu/ftp/ted/book/chap8.pdf
by ted
Mon Aug 26, 2019 1:31 pm
Forum: Getting started
Topic: Current diffusion to nearby sections ?
Replies: 3
Views: 824

Re: Current diffusion to nearby sections ?

I chose to work with individual clamps for each cell, rather than having extracellular stimulation by a single electrode. In other words, using the "activation function" approach to implement stimulation. That won't work for ephaptic interactions between axons, but at least it is a way to stimulate...
by ted
Mon Aug 26, 2019 11:02 am
Forum: NEURON + Python
Topic: Issue with Exp2Syn and stimulation of multiple dendrites
Replies: 3
Views: 769

Re: Issue with Exp2Syn and stimulation of multiple dendrites

the engineering approach that is second nature when it comes to problem solving or looking for a solution One of the reasons why neuroscience needs more engineers. I generally develop code in MATLAB, where I have complete control over all implemented parameters or variables (i.e. when apply a stimu...
by ted
Thu Aug 22, 2019 8:57 pm
Forum: Getting started
Topic: Current diffusion to nearby sections ?
Replies: 3
Views: 824

Re: Current diffusion to nearby sections ?

NEURON simulates neuronal membrane currents and membrane potentials. It does not contain the computational machinery necessary to simulate extracellular potentials produced by extracellular stimulation or by currents generated by neuronal activity. It is possible build models that include such inter...
by ted
Thu Aug 22, 2019 8:48 pm
Forum: NEURON + Python
Topic: Issue with Exp2Syn and stimulation of multiple dendrites
Replies: 3
Views: 769

Re: Issue with Exp2Syn and stimulation of multiple dendrites

When I stimulate Dendrite 1 . . . the Vm potential rises on Dendrites 2, 3 and 4 . . . I have also attempted this with an IClamp . . . I have also attempted going through the NEURON GUI in search for answers by setting up a basic cell in Cell Builder (i.e. soma, axon and 2 dendrites) and stimulatin...
by ted
Wed Aug 21, 2019 9:35 am
Forum: Modeling networks
Topic: "turn off" Netstim in the middle of simulation
Replies: 4
Views: 489

Re: "turn off" Netstim in the middle of simulation

I can use NetCon.active(0) to turn the NetStim events off at&after detected time point. Alternatively, by setting NetCon.weight=0 works similarly. You should probably run a test to make sure that whatever you're doing is working properly. Executing netcon.weight[0] = 0 at some time t should prevent...
by ted
Tue Aug 20, 2019 10:17 am
Forum: Getting started
Topic: multiple pulse current clamp point process
Replies: 2
Views: 849

Re: multiple pulse current clamp point process

Good question. See I just want a current clamp that will deliver a sequence of current pulses at regular intervals. in the FAQ list https://neuron.yale.edu/neuron/faq/general-questions This is also mentioned in the Hot tips area of the forum under How to make IClamp deliver multiple pulses or a wave...
by ted
Mon Aug 19, 2019 2:12 pm
Forum: Modeling networks
Topic: "turn off" Netstim in the middle of simulation
Replies: 4
Views: 489

Re: "turn off" Netstim in the middle of simulation

Not flag. weight. weight is an attribute of a NetCon. Quoting directly from the documentation of NetStim: If, in the on=1 state, the stimulator receives a negative weight event, the stimulator will change to the off state. But to do that, you'd have to create a special NetCon, with negative weight, ...
by ted
Mon Aug 19, 2019 10:10 am
Forum: Modeling networks
Topic: "turn off" Netstim in the middle of simulation
Replies: 4
Views: 489

Re: "turn off" Netstim in the middle of simulation

I already implemented real-time detection part Good. That's the hard part. When the condition "time to turn off the NetStim" happens, use a NetCon's event() method to send an event with weight < 0 to the NetStim that you want to turn off. Read the Programmer's Reference documentation of the NetStim...