Integrating NeuroML 2 with PyNN, Brian & CSA Padraig Gleeson - PowerPoint PPT Presentation

http://www.NeuroML.org Integrating NeuroML 2 with PyNN, Brian & CSA Padraig Gleeson Department of Neuroscience, Physiology and Pharmacology University College London 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Overview • Quick introduction to cells & synapses in LEMS & NeuroML 2 • Incorporating PyNN standard cells into this framework • CSA & PyNN -> NeuroML 2 • NeuroML 2 -> Brian • Future interaction of NineML & LEMS 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Example: Fitzhugh-Nagumo cell model Simplified version of 4 variable HH model 2 state variables, 2 ODEs Image from Scholarpedia.org 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Model expressed in LEMS (Low Entropy Model Original model Specification language) 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Component instance in NeuroML v2.0 A V W 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Adaptive Exponential Integrate & Fire cell 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Incorporating PyNN into NeuroML 2 • PyNN is a Python package for simulator independent specification of neuronal network models • Model code can be developed using the PyNN API and then run using NEURON, NEST, PCSIM, Brian or MOOSE, by replacing: from pyNN.neuron import * with from pyNN.nest import * 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Incorporating PyNN into NeuroML 2 • Initial implementation allowing export of the network structure to NeuroML 2 using: from pyNN.neuroml2 import * • Maps instances of PyNN standard cell models on to equivalent defined in LEMS • Maps populations in PyNN to <population ...> in LEMS • Maps connections generated by PyNN to <explicitConnection ...> in LEMS 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org NeuroML & Connection Set Algebra • PyNN & CSA already well integrated... • Connections described with CSA can be used in PyNN scripts & exported to NeuroML 2 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org NeuroML & Brian interoperability • Brian is a pure Python simulator • Easy to specify new neuron models 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Example 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org LEMS/NeuroML & NineML Much overlap between current NineML abstraction layer & LEMS Component – Component ComponentType – ComponentClass Parameter – Parameter NineML missing key concepts like composition, extension Proposed framework for interaction: Have consistent way to “flatten” LEMS descriptions Useful too for mappings to Brian, MATLAB, SBML... 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

http://www.NeuroML.org Conclusions • Declarative specifications of cell model behaviour useful for cross simulator interoperability • Procedural specification of network structure affords great flexibility • Combination of the two will be useful for moving forward & sharing models 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

Integrating NeuroML 2 with PyNN, Brian & CSA Padraig Gleeson - PowerPoint PPT Presentation

http://www.NeuroML.org Integrating NeuroML 2 with PyNN, Brian & CSA Padraig Gleeson Department of Neuroscience, Physiology and Pharmacology University College London 4 th NeuroML Development Workshop & CodeJam, Edinburgh, March 2012

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