Search found 41 matches

by rth
Mon Feb 01, 2016 1:33 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 16216

Re: Problems installing Neuron on a supercluster

What if I need python?
by rth
Wed Sep 30, 2015 11:18 am
Forum: Getting started
Topic: Choosing random dendrite
Replies: 6
Views: 9122

Re: Choosing random dendrite

Thank you Ted!
That is exactly what I looked for! Wonderful!
by rth
Tue Sep 29, 2015 3:21 pm
Forum: Getting started
Topic: Choosing random dendrite
Replies: 6
Views: 9122

Re: Choosing random dendrite

Thank you Ted! I've got your idea to make a uniform distribution over the surface. I like it more than my previous one. We try to place synapses randomly at some distance from soma to mimic experimental data. So I have bunch of segments trunk[0] ... trunk[79] and apical[1]... apical[98], each of whi...
by rth
Mon Sep 28, 2015 3:57 pm
Forum: Getting started
Topic: Choosing random dendrite
Replies: 6
Views: 9122

Re: Choosing random dendrite

Ted, But code above ensures that one section will have ONLY ONE synapse. It is not truly randomly chosen section from list. For example I want 50 synapses in random sections from SectionList and random position within each section. Position isn't problem, but how I can randomly choose section in Sec...
by rth
Tue Aug 11, 2015 3:43 pm
Forum: Other questions
Topic: Apply extracellular stimulation using electric field
Replies: 16
Views: 9473

Re: Apply extracellular stimulation using electric field

Dear Hyeon, We also tried to use Pashut et al. (2011) TMS model. After few days working with model posted on modeldb, I have found two horrible bugs in the 2D code. The first is that: matlab part of this model generates two matrices 4001x4001 points of Ex and Ey components of electric field. Matlab ...
by rth
Thu Feb 26, 2015 10:57 am
Forum: NEURON + Python
Topic: substitute stadard init() precedure from Python
Replies: 2
Views: 2161

Re: substitute stadard init() precedure from Python

Wonderful! Thanks!
by rth
Wed Feb 25, 2015 5:10 pm
Forum: NEURON + Python
Topic: substitute stadard init() precedure from Python
Replies: 2
Views: 2161

substitute stadard init() precedure from Python

Hi, I need a bit help with NEURON+Python. In hoc file, I can easily write new init procedure and it will be called from the run() function. But how can I substitute standard init() if I use Python? I've tried something like this: def myinit(): h.finitialize() h.fcurrent() h.frecord_init() h.init = m...
by rth
Mon Jun 30, 2014 1:19 pm
Forum: Parallel NEURON
Topic: VecStim in parallel environment
Replies: 4
Views: 10047

Re: VecStim in parallel environment

Thank you, Michael! It works. In other words h.stdinit() should be called just before pc.psolve(), otherwise pc.set_maxstep() won't be initialized and any spike won't be delivered. If this is correct, maybe it will be useful to add pc.pinit( maxstep) function in future version, for calling all requi...
by rth
Mon Jun 23, 2014 3:12 pm
Forum: Parallel NEURON
Topic: VecStim in parallel environment
Replies: 4
Views: 10047

Re: VecStim in parallel environment

In a parallelized implementation of a network model every spike source must be assigned a unique gid. This applies to instances of the VecStim class, which is a class of artificial spiking cell. This involves using ParallelContext's setgid2node method in order to associate the VecStim's gid with th...
by rth
Mon Jun 23, 2014 12:26 am
Forum: Parallel NEURON
Topic: VecStim in parallel environment
Replies: 4
Views: 10047

VecStim in parallel environment

Hi all, I'm writing a code for network which is activated by the input spike trains recorded experimentally or from another model. I load all presynaptic spike events into a vectors and then play these vectors by VecStim-s. Everything worked perfect until I ran simulation on parallel MPI cluster. Su...
by rth
Sat Aug 24, 2013 12:56 pm
Forum: NEURON + Python
Topic: parameters name in inserted modules.
Replies: 3
Views: 2386

Re: parameters name in inserted modules.

Thank you, Ted. I just want set all segments without iterations like in hoc notation: soma g_pas = 0.05 However I've figured out how I can do this in python also: >>> soma = h.Section() >>> soma.insert('pas') <nrn.Section object at 0x96edc08> >>> soma.nseg=7 >>> print soma.g_pas 0.001 >>> for seg in...
by rth
Wed Aug 21, 2013 12:50 am
Forum: NEURON + Python
Topic: parameters name in inserted modules.
Replies: 3
Views: 2386

parameters name in inserted modules.

Hi all, I have strange problem with using NEURON+Python. According Hines et.al. 2009 'NEURON and Python', parameters of inserted modules should be accessible through object's attribute with same name as SUFFIX. soma = h.Section() soma.insert ('pas') soma.pas.g = 0.0003 For example, I inserted a simp...
by rth
Thu Apr 11, 2013 5:18 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

I don't try to connect two of them, but I've tried activate one neuron by Exp2Syn controlled by netstim. So it works. I wouldn't like publish this model on ModelDB until it is properly tested. So you can download it from my webpage http://nisms.krinc.ru/rth/izh/izhcur.zip and test it. I'll very appr...
by rth
Thu Apr 11, 2013 3:15 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

correction: diam should be 1/PI
by rth
Thu Apr 11, 2013 2:36 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

Bill, It seems it works. Here alpha version for testing. Please take a look. I didn't check all 21 modes, but what I've checked works perfect. I'll appreciate for any comments and tests. file izhcur.mod: TITLE IzhikevichCurrent COMMENT This dirty trick implements Izhikevich model as a non-specific c...