Search found 35 matches

by vogdb
Thu Sep 19, 2019 2:24 pm
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 966

Re: Filter Mechanism params by NMODL PARAMETER

That is brilliant! Thank you!
by vogdb
Thu Sep 19, 2019 12:27 pm
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 966

Re: Filter Mechanism params by NMODL PARAMETER

If to be that precise, lets take this example: soma = h.Section(name='soma') soma.insert('hh') for seg in soma: for mech in seg: if mech.name() == 'hh': filtered = [] for n in dir(mech): v = getattr(mech, n) if n.startswith('__') or n in ('next', 'name', 'is_ion', 'segment',): continue filtered.appe...
by vogdb
Thu Sep 19, 2019 7:25 am
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 966

Filter Mechanism params by NMODL PARAMETER

Hello! I'm collecting all cell's mechanisms in Python like this: soma = h.Section(name='soma') // soma.insert( lots of mechanisms ) for seg in soma: for mech in seg: print(mech) mech contains parameters like 'gbar', 'g', 'ica' and so on. How can I filter them to get only those that are in 'PARAMETER...
by vogdb
Wed Sep 11, 2019 12:07 pm
Forum: NEURON + Python
Topic: Export to .hoc with CellBuilder from Python
Replies: 2
Views: 1330

Re: Export to .hoc with CellBuilder from Python

Thank you for the response.
by vogdb
Tue Sep 10, 2019 12:32 pm
Forum: NEURON + Python
Topic: Export to .hoc with CellBuilder from Python
Replies: 2
Views: 1330

Export to .hoc with CellBuilder from Python

Hi! I'm trying now for a week to properly export the currently loaded neuron model. There is only one loaded model in my namespace that I loaded like this. h.load_file('Cell_Scnn1a.hoc') cell_hoc = h.Cell_Scnn1a('/morphologies', 'Scnn1a_473845048_m.swc') It is absolutely properly exported to nml by ...
by vogdb
Wed Sep 04, 2019 6:42 am
Forum: NEURON + Python
Topic: Save model's biophysics and morphology programmatically to .hoc
Replies: 3
Views: 663

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

I've managed to export it into a single nml file. h.load_file('Cell_Scnn1a.hoc') cell_hoc = h.Cell_Scnn1a('/morphologies', 'Scnn1a_473845048_m.swc') h.load_file("mview.hoc") mv = h.ModelView(0) mv_xml = h.ModelViewXML(mv) export_filepath = os.path.join('.', 'test.nml') mv_xml.exportNeuroML(export_fi...
by vogdb
Tue Sep 03, 2019 3:26 pm
Forum: NEURON + Python
Topic: Save model's biophysics and morphology programmatically to .hoc
Replies: 3
Views: 663

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

Am I correct that I would need to call proc exportNeuroML from share/lib/hoc/mview/mviewxml.hoc ?
by vogdb
Tue Sep 03, 2019 11:25 am
Forum: NEURON + Python
Topic: Save model's biophysics and morphology programmatically to .hoc
Replies: 3
Views: 663

Save model's biophysics and morphology programmatically to .hoc

Hi! I couldn't find the answer in similar topics: https://www.neuron.yale.edu/phpBB/viewtopic.php?t=1855 , https://www.neuron.yale.edu/phpBB/viewtopic.php?t=364 . I have a model loaded from this kind of template: {load_file("stdrun.hoc")} {load_file("import3d.hoc")} begintemplate Cell_Scnn1a public ...
by vogdb
Thu Aug 22, 2019 3:34 am
Forum: NEURON + Python
Topic: Does Section have something like `id` attribute?
Replies: 2
Views: 668

Re: Does Section have something like `id` attribute?

Thank you for such a thorough answer! By any chance, do you have an example of identifying sections in parallel environment?
by vogdb
Wed Aug 21, 2019 12:16 pm
Forum: NEURON + Python
Topic: Does Section have something like `id` attribute?
Replies: 2
Views: 668

Does Section have something like `id` attribute?

Hello everyone! I'm trying to launch a Sonata network in NEURON. According to their documentation they store synapses locations as some section id. I suspect that it is a Section's index in h.allsec() collection. I've looked over Section's documentation and have some questions. 1. Am I correct that ...
by vogdb
Thu Aug 15, 2019 1:43 pm
Forum: NEURON + Python
Topic: Convert Python to Hoc
Replies: 4
Views: 1019

Re: Convert Python to Hoc

For now I couldn't do it. Currently jNeuroML does not support json files. I have to make it by hands unfortunately, can't waste time on this anymore.
by vogdb
Thu Aug 15, 2019 6:45 am
Forum: NEURON + Python
Topic: Convert Python to Hoc
Replies: 4
Views: 1019

Re: Convert Python to Hoc

Seems that https://github.com/NeuroML/jNeuroML is a way to go.
by vogdb
Wed Aug 14, 2019 2:24 pm
Forum: NEURON + Python
Topic: Convert Python to Hoc
Replies: 4
Views: 1019

Convert Python to Hoc

Hello! There is a model https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=184187 . It exists in NeuroML2 and standalone Python versions. Is it possible to convert any of these into Hoc? What would you suggest? Would it be simpler just to recreate Hoc file from scratch? My circumstances ar...
by vogdb
Mon Oct 23, 2017 10:47 am
Forum: Getting started
Topic: Please recommend a book about simplification of detailed neuron models for the simulation of large networks
Replies: 4
Views: 10558

Re: Please recommend a book about simplification of detailed neuron models for the simulation of large networks

Thank you so much! I completely agree with you about conceptual model. The funny thing is that I chose an example of "rate vs spike timing" randomly and I am more interested in other things: 1. How to collapse a huge compartmental model into a IAF-like neuron. 2. What to do with multiples channels d...