Padraig GleesonOSB Workshop 2014

Enabling sharing & collaborative development of models in computational neuroscience

Thanks to our sponsors

Overview

Open Source Brain

NeuroML v2.0 & LEMS

Collaborative Modelling

The Open Source Brain Repository

Wellcome Trust funded project

Open source model development repository for computational neuroscience

Structured database of well tested spiking neuron & network models in standardised formats

Allow anyone to comment on, extend, reuse models & run them across multiple simulators: a collaboration platform

Uses tools & best practices from Open Source software development

Models available on OSB

NeocortexMainen et al. (1995)

L5 Pyramidal cellRothman et al. (2010)

L5 Pyramidal cellHay et al (2011)

L5 Pyramidal cellTraub et al. (2005)

L2/3 Pyr (FRB/RS), L4SS, L5 Pyr (IB/RS), L6 Pyr,Deep & superficial basket, axo-axonic & LTS interneurons,Cortical column network model

CerebellumMaex and Schutter (1998)

Granule cell layerSteuber and Saviane, based on Berends et al. (2005)

Granule cellVervaeke et al. (2010)

Golgi cell networkSolinas et al. (2007a,b)

Granule cell, Golgi cellDe Schutter and Bower (1994)

Purkinje cellSteuber et al. (2011)

Cerebellar nucleus neuron

Basal GangliaBlackwell et al (in press)

Medium Spiny Neuron

ThalamusTraub et al. (2005)

Thalamocortical relay cell,Nucleus reticularis thalami cell

HippocampusMigliore et al. (2005)

CA1 Pyramidal cell

Abstract neuron modelsIzhikevich (2003)Morris & Lecar (1981)FitzHugh & Nagumo (1969)

C elegans

OpenWorm project302 cell connectome

Version control & GitHub

“Version control is as fundamental to programmingas accurate notes about lab procedures are toexperimental science”(G. Wilson, 2006. Where's the Real Bottleneck in Scientific Computing?)

CVS → SVN → Mercurial/Git

GitHub– Most popular open source code sharing website– “Social coding”

“Hub and Spoke” architecture

NeuroML

Standardised XML language for computational neuroscience

Version 1.x allowed specification of:– Detailed neuronal morphologies– Ion channels– Synapses– 3D network structure

30+ simulators/applications/databases/libraries support NeuroML

Cells

Channels/Synapses

Network

http://www.opensourcebrain.org

NEURON GENESIS MOOSE PSICS NeuroSpaces

PyNN neuroConstruct

Whole BrainCatalog

LFPy

NeurAnimNeuronvisio Moogli NeuronLand

TREES toolbox

NeuGenNeuroMorpho Channelpedia

OpenWorm TrakEM

CX3D

NeuroML v2.0 & LEMS

Example model: current through a passive channel

NeuroML v2.0 & LEMS

LEMS

http://www.opensourcebrain.org

OSBModel

Repository

Collaborative development

BioModels

OSBModel

Repository

Search

ModelDB

Projects

Modellers

Visualisation

Testing

Validation

Annotation

Conversion

PyNN

Simulators

Feedback from the Community

Simulators

Acknowledgements Silver Lab @ UCL

Angus Silver

Eugenio Piasini

Boris Marin

Adrian Quintana

Matteo Farinella

Yates Buckley

Matteo Cantarelli

Main Collaborators Robert Cannon

Sharon Crook

Mike Vella

Early Adopters Sergio Solinas

Egidio D'Angelo

Volker Steuber

Dieter Jaeger

Andrew Davison

Stephen Larson

Avrama Blackwell

Nicolas Le Novere

Funding source:

Members of the NeuroML community

OpenWorm project

UK INCF Node