Chair: Angus SilverUniversity College London

INCF - Neuroinformatics 2014

WORKSHOP 4

Open collaboration in computational neuroscience

Neuronalclasses

How can we scale up models of brain function and make models more accurate and reproducible?

100 billion neurons100 trillion synapses

Specialized networks

Synaptic types

Input about the body and world

Sensations

Cognition

Actions

Electrical

Chemical

Conventional model development

Expe

rim

ent

Impl

emen

t th

e m

odel

and

tune

it

Publ

ish

0.1 0.2 0.3 1.0...

Cle

an u

p

1.1.1.1

1.1.1.2

Requirements I: A culture change –collaborative development

Publ

ish

1.0...

LAB A

Upd

ate

LAB B

1.1.1

tU

pdat

e1.1

LAB C

1.1.3

Upd

ate Upd

ate

Mer

ge

1.2

Mer

ge

Requirements II: datasets, tools, standardization, and open scientific

evaluation

Tools for collaborative model development

Open source development tools- GitHub Simulators – e.g. Neuron, Brian Applications – e.g. neuroConstruct, Neurokernel, NeuronUnit

Standardized model descriptions

SBML, CellML, NineML, SpineML

Accessibility and critical evaluation

ModelDB, BioModels etc

Open Source Brain

Datasets

NeuroMorpho

Pros and Cons of open development and collaboration in

neuroinformatics

Potential Benefits•Scaling up of modeled systems•Continuity of projects•Improved community resources •Development of integrated tool chain•Improved scientific value through improved :•Reproducibility, •Accessibility,•Portability•Transparency

Difficulties/Issues

• Neuroscience is a competitive system.•Vested interests - can we change the prevailing culture?• Big investment to develop the tool chain. •How will quality be ensured?•Will the efforts of the developers be adequately recognized?•Are computational neuroscientists ready to expose all the flaws of a model to public scrutiny?

10:20 Introduction : Angus Silver, UCL, UK

10:30 OpenWorm - Stephen Larson, MetaCell, USA

10:50 Open Source Brain - Padraig Gleeson, UCL, UK

11:10 NeuronUnit & NeuroElectro - Rick Gerkin, Carnegie Mellon University, USA & Shreejoy Tripathy, University of British Columbia, Canada

11:35 NeuroKernel - Aurel A. Lazar, Columbia University, USA

11:55 Conclusions/Discussion

WORKSHOP 4

Open collaboration in computational neuroscience

Open collaboration in computational neuroscience

Discussion – how to address the issues...?

➢Neuroscience is a competitive system.➢Vested interests - can we change the prevailing culture?➢Big investment to develop the tool chain. ➢How will quality be ensured?➢Will the efforts of the developers be adequately recognized?➢Are computational neuroscientists ready to expose all the flaws of a model to public scrutiny?

Synapse

Network

Neuron

Molecular assemblies

Brain

Genes

Biologically accurate multi-scale models of brain function.

Modelling brain function at different spatial scales