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NeuralEnsemble / Networks_SIG

INCF SIG on Standardised Representations of Network Structures
https://www.incf.org/sig/standardised-representations-network-structures
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Extend NeuroML to incorporate rate based/neural mass models #4

Open pgleeson opened 5 years ago

pgleeson commented 5 years ago

Much work has already taken place for this in the GSoC for OSB: http://neuralensemble.blogspot.com/2018/08/neuroml2lems-is-moving-into-neural-mass.html

This work has involved expressing neural masses/population units in LEMS format to encapsulate the dynamics of the rate changes. Links for projects with neural mass models in LEMS: https://github.com/OpenSourceBrain/WilsonCowan https://github.com/OpenSourceBrain/del-Molino2017 https://github.com/OpenSourceBrain/MejiasEtAl2016

Eventually some or all of these models could/should be mapped onto The Virtual Brain format.

JohnGriffiths commented 5 years ago

Re: mapping to TVB format - there is some functionality implemented in TVB for specifying simulations from .json .

e.g.

https://github.com/the-virtual-brain/tvb-documentation/blob/master/demos/sandbox/load_simulation_from_json.ipynb

It's still quite rudimentary and possibly buggy, but a useful direction might be to figure out the correspondences between this .json structure and the neuroml .xml structure.

pgleeson commented 5 years ago

Relevant for TVB: https://github.com/maedoc/tvb-lems

pgleeson commented 5 years ago

Another potential target simulation/analysis tool for these models: https://github.com/breakspear/bdtoolkit