Search found 41 matches

by rth
Wed Jul 29, 2020 2:11 pm
Forum: Other questions
Topic: initialization of calcium concentration in a segment with attached point process
Replies: 5
Views: 8567

Re: initialization of calcium concentration in a segment with attached point process

Dear Ted, Thank you so much, for your very helpful comments and suggestions. I saw the problem with the INITIAL block in the CaDynamics_E2 module but somehow ignored it. We need to control cao, because, it seems extracellular calcium concentration drifts during the development period. I implemented ...
by rth
Mon Jul 27, 2020 1:59 am
Forum: Other questions
Topic: initialization of calcium concentration in a segment with attached point process
Replies: 5
Views: 8567

initialization of calcium concentration in a segment with attached point process

I have a model of a V1 pyramidal neuron, with simplified morphology. Somatic, basal and apical compartments have calcium channels and calcium dynamics. Zip archive with all mod files and test-model example can be downloaded here https://storage.r-a-r.org/index.php/s/jLCz6m4k3TXFgmK Only a few channe...
by rth
Sun Nov 24, 2019 10:54 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: where to declare cai and cao ?
Replies: 1
Views: 2759

where to declare cai and cao ?

Dear all, My question is somehow related to the Pascal's question https://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=4084 because, it seems, I stumbled to a similar problems. I'm trying to play around with Iavarone's model, which uses the same old Destexhe's code https://senselab.med.yale.ed...
by rth
Tue Dec 11, 2018 11:53 am
Forum: Parallel NEURON
Topic: Strange NEURON behavior with multithreading
Replies: 0
Views: 11166

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: 16318

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: 16318

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: 16318

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: 16318

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: 16318

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: 11154

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: 11154

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: Parallel NEURON
Topic: h.fadvance() stops python threading, why?
Replies: 2
Views: 15577

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: Parallel NEURON
Topic: h.fadvance() stops python threading, why?
Replies: 2
Views: 15577

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: 28251

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: 20125

Re: Problems installing Neuron on a supercluster

Thank you! I'll try to play with it or work around.