Search found 33 matches

by Yaeger
Wed Apr 10, 2019 11:48 am
Forum: Optimization
Topic: Optimization of single cell models
Replies: 3
Views: 1529

Re: Optimization of single cell models

Okay, good point. I mean average membrane potential (say over one cycle of oscillation) by rest. The trouble is I am trying to constrain at least some of my channel kinetics to the experimentally measured values (at the soma in a pyramidal-type cell with terrible space clamp). The real cells that I'...
by Yaeger
Fri Apr 05, 2019 11:50 am
Forum: Optimization
Topic: Optimization of single cell models
Replies: 3
Views: 1529

Optimization of single cell models

Hi, I am trying to optimize a model of an oscillating single-compartment neuron to get it to oscillate (and "rest") at a specific membrane potential. I've written python code to create a class for my neuron (using Neuron) and then by creating hundreds of thousands of instances of the model with para...
by Yaeger
Fri Mar 15, 2019 6:20 pm
Forum: NEURON + Python
Topic: How to use a fixed time-step in Python?
Replies: 2
Views: 1621

Re: How to use a fixed time-step in Python?

Thank you Ted!
by Yaeger
Thu Mar 14, 2019 5:59 pm
Forum: NEURON + Python
Topic: How to use a fixed time-step in Python?
Replies: 2
Views: 1621

How to use a fixed time-step in Python?

How do you use a run method with a fixed time-step in python?
by Yaeger
Mon Dec 24, 2018 1:10 pm
Forum: UNIX/Linux
Topic: Which version of Neuron works with Python 2.7?
Replies: 1
Views: 1277

Which version of Neuron works with Python 2.7?

Hi, I'm trying to install python on a linux server running Python 2.7. What is the latest version of Neuron that is compatible with Python 2.7? Thanks!
by Yaeger
Mon Dec 17, 2018 8:19 pm
Forum: Specific models
Topic: Single-compartment deterministic oscillating cell model?
Replies: 2
Views: 1984

Re: Single-compartment deterministic oscillating cell model?

Sorry, here's the Ih gating parameters, which I had to tweak a bit from the published equations to get them to resemble the fits in Fig. 11C: mInfFast = 1.0/(1 + exp((v + 67.4)/12.66)) mInfSlow = 1.0/(1 + exp((v + 57.92)/9.26)) mAlphaFast = (0.3*(2.89e-3*v -0.445))/(1 - exp((v + (0.445/(2.89e-3)))/2...
by Yaeger
Mon Dec 17, 2018 8:17 pm
Forum: Specific models
Topic: Single-compartment deterministic oscillating cell model?
Replies: 2
Views: 1984

Single-compartment deterministic oscillating cell model?

Hi, I am trying to implement a published single compartment-model in Neuron or Matlab that is not available on Modeldb: CLAYTON T. DICKSON, JACOPO MAGISTRETTI, MARK H. SHALINSKY, ERIK FRANSEN, MICHAEL E. HASSELMO, AND ANGEL ALONSO1Properties and Role of Ih in the Pacing of Subthreshold Oscillations ...
by Yaeger
Thu Apr 10, 2014 6:48 pm
Forum: Other questions
Topic: randomization of simulation execution
Replies: 1
Views: 739

randomization of simulation execution

Hi, I am running a network simulation that makes use of the ranstream.hoc file from "The Randomness in Neuron Models" entry in the Documentation section on the website to connect neurons as in Hines & Carnevale, 2008 J Neurosci Methods. What I would like to now do is randomization of simulation exec...
by Yaeger
Wed Dec 18, 2013 8:22 pm
Forum: Other questions
Topic: NetStim Event Times Same from Trial to Trial?
Replies: 4
Views: 1749

Re: NetStim Event Times Same from Trial to Trial?

Now I am seeing that there is a problem with this code, although I am not sure where it is. For random seeds between zero and one, the NetStim generates the same interevent intervals.
by Yaeger
Wed Dec 18, 2013 7:10 pm
Forum: Other questions
Topic: NetStim Event Times Same from Trial to Trial?
Replies: 4
Views: 1749

Re: NetStim Event Times Same from Trial to Trial?

Hi Ted - Thanks for the quick and helpful reply. Sorry it has taken me a bit to reply. Per your advice I have generated some code to create a vector of random numbers using Random123. objref r r = new Random() r.negexp(1) r.Random123(1) objref rvec rvec = new Vector() proc genran() { local i, seed f...
by Yaeger
Tue Dec 10, 2013 5:27 pm
Forum: Other questions
Topic: NetStim Event Times Same from Trial to Trial?
Replies: 4
Views: 1749

NetStim Event Times Same from Trial to Trial?

Hi, I am using NetStim to generate poisson-distributed event times to drive synapses. To my surprise, everytime I run the simulation the NetStim events seem to be occurring at the same time. I would have thought that the poisson-distributed event times would be generated probabilistically every time...
by Yaeger
Tue Dec 10, 2013 4:27 pm
Forum: Other questions
Topic: Averaging Synaptic Current Between Specific Times
Replies: 1
Views: 1259

Averaging Synaptic Current Between Specific Times

Hi, I would like Neuron to give me a readout of the synaptic current that a neuron receives. Ordinarily, this would be easy because you could record the synaptic current(s) in a vector and then just average the contents of the vector. However, in my simulations the synaptic currents begin at a parti...
by Yaeger
Wed Nov 27, 2013 2:17 pm
Forum: Other questions
Topic: Mechanisms not accessible in template
Replies: 3
Views: 1223

Re: Mechanisms not accessible in template

Thanks Ted. I am now testing the template against the otherwise identical non-templated hoc file specifying the cell.
by Yaeger
Wed Nov 27, 2013 2:16 pm
Forum: Other questions
Topic: Mechanisms not accessible in template
Replies: 3
Views: 1223

Re: Mechanisms not accessible in template

I believe that I have solved the problem by including an init command in the template file: begintemplate Granule public soma create soma proc init() { create soma soma { nseg=1 diam=11.8 L=11.8 Ra=100 cm=1 insert GRC_LKG1 insert GRC_NA insert GRC_KV } } endtemplate Granule Now, after creating a new...
by Yaeger
Tue Nov 26, 2013 4:08 pm
Forum: Other questions
Topic: Mechanisms not accessible in template
Replies: 3
Views: 1223

Mechanisms not accessible in template

Hi, I am trying to create a template of a cell class in hoc. The only variable that I am declaring as public is soma, which contains all of the channel mechanisms. When I create an object from the template in Neuron, it clearly only has a capacitor (i.e. Neuron is not "seeing" the channels inserted ...