[neuroConstruct] Neuroconstruct for dolphin ear canal?

[Gleeson, Padraig]

Hi Steffen,

neuroConstruct could be helpful for some parts of your study, but unfortunately not all. It should be good for developing models in 3D of the network, either imported from neuronal reconstructions, or "manually" (and unfortunately slightly tediously) with abstract cells built section by section in the GUI; it should allow you to add channel distributions to the cells to create spiking models; can help you generate code in Neuron (and other simulators, but I'd target this one) for running simulations, and you can view/analyse the activity back in nC.

It won't help you with any other types of 3D interaction of the network with physical entities, and unless there is an existing example of the cell you would like in neuroConstruct (unlikely) or even Neuron (check on ModelDB<https://senselab.med.yale.edu/ModelDB/default.cshtml>) it might be a slow process to create the network. Nevertheless it should be possible, see here for more instructions: http://www.neuroconstruct.org/docs/importneuron.html

What I'd recommend is assembling any model code you can find out there for the various pieces you need and maybe making Python the language to tie these together. There are scripting interfaces for most simulators in Python, and if you do want to make the core network simulator independent, you could express it in NeuroML using the Python API libNeuroML<https://github.com/NeuralEnsemble/libNeuroML>. Once it's in NeuroML this will enable the model to be displayed (and simulated) on Open Source Brain (for more advice on this see here<http://www.opensourcebrain.org/docs#Converting_To_NeuroML2>). OSB these days replicates much of the functionality of the desktop based neuroConstruct...

Hope this helps,

Regards,

Padraig


On 11/02/2019 16:36, Steffen De Vreese wrote:
Dear Mr. Gleeson,

My name is Steffen, I am a Ph.D. student in Veterinary and Marine Sciences, and I study the peripheral nervous system of dolphins, with a focus on the external ear canal. Surrounding this canal, there is a very complex network of mechanoreceptors, nerves and free endings. I am considering NeuroConstruct as a possible useful application to study this network, but I cannot seem to find any similar study in the literature/online.
Could you please give some more information on whether NeuroConstruct could be useful in this regard? If you please, I can give more information on the system I am studying.

With kind regards,
Steffen

--
Steffen De Vreese, MVM, Doctoral candidate
Dipartimento di Biomedicina Comparata e Alimentazione (BCA) - Università degli Studi di Padova (It)
Laboratori d'Aplicacions Bioacústiques (LAB) - Universitat Politécnica de Catalunya (Es)
steffen.devreese at studenti.unipd.it<mailto:steffen.devreese at studenti.unipd.it>
steffen.devreese at lab.upc.edu<mailto:steffen.devreese at lab.upc.edu>
Linkedin.com/in/steffen-de-vreese-033a5994
Researchgate.net/profile/Steffen_De_Vreese
Skype: devreesesteffen



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Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
University College London
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+44 207 679 3214
p.gleeson at ucl.ac.uk<mailto:p.gleeson at ucl.ac.uk>
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