Search found 38 matches

by rth
Tue Dec 11, 2018 11:53 am
Forum: NEURON + Python
Topic: Strange NEURON behavior with multithreading
Replies: 0
Views: 697

Strange NEURON behavior with multithreading

Dear NEURON developers, I have run into a very strange NEURON behavior, which I couldn't understand. It relates to the multithreading, but perhaps I did something stupid. I have a simple mod mechanisms UNITS { (mA) = (milliamp) (mV) = (millivolt) (mS) = (millisiemens) } NEURON { SUFFIX nak3dv02 NONS...
by rth
Thu Jul 13, 2017 1:43 am
Forum: NEURON + Python
Topic: Any simple way to identify parent segment of point porcess
Replies: 8
Views: 10644

Re: Any simple way to identify parent segment of point porce

ramcdougal, I see your point.

Yes, you are right, it is tricky but may work. Actually very good idea. Of course, it is 'workaround', and it will be better to have a direct way inside NEURON+Python module, but it is nice to have a solution. Let me try :)
by rth
Thu Jul 13, 2017 1:31 am
Forum: NEURON + Python
Topic: Any simple way to identify parent segment of point porcess
Replies: 8
Views: 10644

Re: Any simple way to identify parent segment of point porce

Very good point! Thank you!
But how will you use this list to setup point process? Maybe we can use float point position as segment #/nseg ? But this should link somehow to NEURON inner mechanism of position float point resolving.
by rth
Wed Jul 12, 2017 10:47 pm
Forum: NEURON + Python
Topic: Any simple way to identify parent segment of point porcess
Replies: 8
Views: 10644

Re: Any simple way to identify parent segment of point porce

ramcdougal , thank you, for the suggestion! That is a very neat solution. But if we start from accuracy and electrical length, the number of segments is a constant, unless my dendrites start growing. From this point of view, the best strategy to minimize the amount of computation is to be sure that...
by rth
Wed Jul 12, 2017 10:17 pm
Forum: NEURON + Python
Topic: Any simple way to identify parent segment of point porcess
Replies: 8
Views: 10644

Re: Any simple way to identify parent segment of point porce

Thank you, Ted, unless they belong to instances of an event-driven point process class (synaptic mechanism) that can be driven by multiple input streams, and you want to exploit that property in order to reduce model complexity and speed up simulations. Which apparently is rth's aim. As you know fro...
by rth
Mon Jul 10, 2017 7:30 pm
Forum: NEURON + Python
Topic: Any simple way to identify parent segment of point porcess
Replies: 8
Views: 10644

Any simple way to identify parent segment of point porcess

Dear All, I apologize for a very trivial question. I have a python class which reconstructs neuron morphology from an SWF file, sets channels and so on. Now with such a nice reconstruction, I need to create 6k - 10k synapses on dendrite tree. Moreover, there are about 5 different synapses classes, w...
by rth
Tue Jun 20, 2017 3:17 pm
Forum: NEURON + Python
Topic: Gradual change of synaptic weights for mimicking neuromod...
Replies: 2
Views: 9463

Re: Gradual change of synaptic weights for mimicking neuromo

A vector instance can play into only one reference variable. So if there are a lot of them and only a few modulation instances, it may be more efficient to modify the synapse so the NET_RECEIVE block multiplies the weight argument by a POINTER to one of a small number of modulation values per threa...
by rth
Mon Jun 12, 2017 11:49 pm
Forum: NEURON + Python
Topic: Gradual change of synaptic weights for mimicking neuromod...
Replies: 2
Views: 9463

Gradual change of synaptic weights for mimicking neuromod...

I want to model a gradual change in synaptic conductance due to changing in concentration of some neuromodulator. I have a list of connections. Each element of the list is a tuple of (NetCon, presynaptic index, postsynaptic indexes). Now I'm trying to use Vector.play, to change synaptic weight durin...
by rth
Thu May 11, 2017 7:17 pm
Forum: NEURON + Python
Topic: h.fadvance() stops python threading, why?
Replies: 2
Views: 9180

Re: h.fadvance() stops python threading, why?

Thank you, for reply. Well, it isn't fortune. I'm trying to run a quite long simulation (minutes) and of course memory couldn't hold all generated data. So the idea was to run a simulation for one second, copy all vectors into python and resume a simulation, while python saves data on disk. It isn't...
by rth
Tue May 09, 2017 4:35 pm
Forum: NEURON + Python
Topic: h.fadvance() stops python threading, why?
Replies: 2
Views: 9180

h.fadvance() stops python threading, why?

Hi all, I have a bit strange problem with using threading Python module with NEURON. I run NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09 from Python 2.7.12 (default, Nov 19 2016, 06:48:10) script under Linux 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/...
by rth
Thu Feb 09, 2017 9:57 pm
Forum: Specific models
Topic: NEURON implementation of Compte et al 2003 pyramidal cell
Replies: 0
Views: 14844

NEURON implementation of Compte et al 2003 pyramidal cell

Hi everyone,

I'm looking for implementation of two compartment pyramidal cell model from Compte et al 2003 in NEURON.
http://jn.physiology.org/content/89/5/2707.long

Couldn't find anything, even similar, in Model DB.
Thank you,
rth
by rth
Mon Feb 22, 2016 11:56 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 13955

Re: Problems installing Neuron on a supercluster

Thank you! I'll try to play with it or work around.
by rth
Mon Feb 01, 2016 1:33 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 13955

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: 8474

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: 8474

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...