GSoC 2021 project idea 12.1: Open source, cross simulator, large scale cortical models in NeuroML and PyNN

An increasing number of studies are using large scale network models incorporating realistic connectivity to understand information processing in cortical structures. High performance computational resources are becoming more widely available to computational neuroscientists for this type of modelling and general purpose, well tested simulation environments such as NEURON and NEST are widely used. New, well annotated experimental data and detailed compartmental models are becoming available from the large scale brain initiatives. However, the majority of neuronal models which have been published over the past number of years are only available in simulator specific formats, illustrating a subset of features associated with the original studies.

This work will involve converting a number of published large scale network models into open, simulator independent formats such as NeuroML and PyNN and testing them across multiple simulator implementations. They will be made freely available to the community through the Open Source Brain repository (http://www.opensourcebrain.org) for reuse, modification and extension.

Skills required: Python; XML; open source development; a background in computational/theoretical neuroscience and/or large scale modelling experience.

Aims:

  1. Select a number of large scale cortical network models for the conversion & testing process (e.g. from ModelDB).

  2. Convert network structure and cell/synaptic properties to NeuroML and/or PyNN. Where appropriate use the simulator independent specification in LEMS to specify cell/synapse dynamics & to allow mapping to simulators. Implementing extensions to PyNN, NeuroML or other tools may be required.

  3. Make models available on the Open Source Brain repository, along with documentation and references.

Mentors: Padraig Gleeson @pgleeson (lead), Ankur Sinha @sanjayankur31

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Hi, Mohit here. I am a sophomore in Mathematics at IIT Kanpur in India. I would like to know more about the project and to work on it.

Previously I have been working with the Svoboda Lab on models of learning and plasticity. Specifically, I was initially interested in backpropagation like bio-plausible learning algorithms like Target Prop, Feedback Alignment, etc. Recently I have worked a lot on models that are more or less Hebbian in nature and work towards the dynamics of such systems.

I have experience in neuroscience through coursework(Neurobiology, Computational Cognitive Science) as well as through lab-related work. Let me know how I should approach this project and what all is required of off me.

My GitHub: m2kulkarni (Mohit Kulkarni) · GitHub

Tagging Mentors: @pgleeson and @sanjayankur31

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Hi Mohit,
Thanks for your interest. I’ll add more info shortly after INCF gets accepted as an official organisation, but it will be similar advice to last year, see here: GSoC 2020 project idea 10: Open source, cross simulator, large scale cortical models - #4 by pgleeson.
Regards,
Padraig

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