GSoC Project Idea 5: Open source, cross simulator, large scale cortical models

python
xml
networks
modelling
simulation

#1

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 associates 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.

Required skills: Python; XML; open source development; computational modelling experience.

Desired skills: Java experience; a background in theoretical neuroscience and/or large scale modelling.

Aims:

  1. Select a number of large scale cortical network models for the conversion & testing process.
  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.

Mentor: Padraig Gleeson, Open Source Brain, UK.

Keywords: Python, XML, networks, modelling, simulation