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