Neuroinformatics in the United Kingdom David Willshaw Institute for Adaptive & Neural Computation...
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Transcript of Neuroinformatics in the United Kingdom David Willshaw Institute for Adaptive & Neural Computation...
Neuroinformatics in the United Kingdom
David WillshawInstitute for Adaptive & Neural Computation
School of InformaticsUniversity of Edinburgh, UK
Summary of talk
1. Definition of Neuroinformatics
2. How to Organise Neuroinformatics on a National and an International Scale
3. Neuroinformatics Activities in the UK- the science
4. Neuroinformatics Activities in the UK- organisation
5. Neuroinformatics Related Activities/Events/Schemes
6. Self-reflection: Lessons for the UK
1. Definition of Neuroinformatics
Neuroinformatics
“… Combines neuroscience and informatics research to develop and apply the advanced tools
and approaches that are essential for major advances in understanding the structure and
function of the brain.”
Report of the OECD Megascience Forum Biological Informatics Working Group Neuroinformatics Subgroup,
1998
The three pillars of neuroinformatics
NEUROSCIENCE
DATA & DATABASES
SOFTWARE
TOOLS
COMPUTATIONAL
NEUROSCIENCE
Analysis
Simulation
GENERAL COMPUTATIONAL
PRINCIPLES
2. How to Organise Neuroinformatics on a National and International Scale
Possible ways of integrating neuroinformatics worldwide
1. Centralised
• Has a physical Centre, to which all other geographical units are related as satellites
• Simple structure (and management?)
• ‘Easy’ to justify to national funding bodies, especially if there is a local central mass of expertise
• Dominated by Centre, requiring satellites to buy in on the Centre’s terms
Possible ways of integrating neuroinformatics worldwide
2. Federated
• Many equal partners • Distributed management, with minimal central
coordination• Covers many geographical regions and all of
neuroinformatics• No insistence on common standards• To be plausible to national funding bodies this requires
lots of real international collaborations • Loose management structure may be a drawback
Possible ways of integrating neuroinformatics worldwide
3. Local first, global afterwards
• Easier to form a committed local community then a committed global one
• Easier to deal with local concerns locally • Easier to argue for generic methodologies locally than
globally• But how to do the joining up?
These models have been proposed – what has happened?
1. Centralised: lacks wide international commitment to particular aims of project
2. Federated: its focus had to be made much narrower than initially envisaged, to satisfy the funding agency but making it less satisfactory to the neuroinformatics community at large
3. Local first, global afterwards: we must all try to get the local bit right first
3. Neuroinformatics Activities in the UK- the science
The mechanism for the propagation of the impulse (1952)
A L Hodgkin and A F Huxley, J. Physiol., 117, 500-544 (1952)
Conductance is voltage-dependent….
Marr’s (1969) model for the role of the cerebellum in associative learning
Features of UK neuroinformatics
From Sept 2001 workshop
Features: • lots of modelling work (hippocampus, basal ganglia, visual system,
developmental), brain imaging, a few databases (eg, for Drosophila), small but significant activity in tools
Concerns: • long term support of neuroinformatics tools• lack of credit assigned to neuroinformatics practitioners• standards: cottage industry preferred over Microsoft model• need to compete for funding with strong UK bioinformatics community• little track record in industrial/commercial collaboration• coordination of the various UK funding schemes desirable
4. Neuroinformatics Activities in the UK- organisation
• The three most relevant of the seven UK Research Councils:
• MRC – Medical Research Council (£490M p.a)
• BBSRC – Biotechnology and Biological Sciences Research Council (£270M p.a.)
• EPSRC – Engineering and Physical Sciences Research Council (£560M or 800MEuro p.a.)
Steps towards developingUK neuroinformatics
1996
1999
2001
• Workshop in Edinburgh to inform MRC Neurosciences and Mental Health Board
• EPSRC/MRC/BBSRC workshop in Abingdon bringing together neuroscientists, biologists and computer scientists with funding agencies
• MRC/EPSRC workshop in Edinburgh attended by ~50 neuroinformaticians and potential neuroinformaticians
Steps towards developingUK neuroinformatics
2004
- 2007
• ESRC/MRC/BBSRC funded
Network in Neuroinformatics
Goals of the Network:– To establish the community– To examine state of UK neuroinformatics– To scope out areas of likely development
– This will act as the UK node in the OECD recommended scheme
UK Neuroinformatics Network work plan
5. Neuroinformatics Related Activities/Events/Schemes
Activities/events/schemes specific to neuroinformatics
1999-
2002- 2004
2000 - 2002
2002- 2007
2002- 2005
• Neuroinformatics PhD studentships/fellowships (MRC)
• Summer school in neuroinformatics (EPSRC)
• Workshops on high performance neuroinformatics (EPSRC/MRC)
• Programme Grant in computational neuroscience (MRC)
• eScience grant on computational tools for neuroinformatics (MRC/BBSRC)
Activities/events/schemes with a wider remit
2001
- 2004
2002
- 2003
• £120M UK Government Initiative in eScience
(eScience: “science undertaken through distributed global collaborations enabled by the Internet, involving large of complex data collections, terascale computing resource and high performance visualisation”)
• UK Government Foresight Initiative in Cognitive Systems– Initiative by scientists that brings together life scientists, computer
scientists/engineers to help each other • to understand (natural) cognitive systems• to build better (artificial) cognitive systems
Activities/events/schemes with a wider remit
2001
2002- 2003
2002- 2003
2003
2003
• EPSRC Life Sciences Interface Programme established
– £20M call for research into Novel Computation• 16 clusters of scientists given funding to develop proposals
– £35M Doctoral Training Programme in the Life Sciences• 7 centres established, each offering 50 4-year PhD studentships
in subjects at the intersection of the life sciences and the physical/computer sciences, maths & engineering
– The centre at Edinburgh is dedicated to neuroinformatics– Two other neuroinformatics related centres (biological modelling,
UCL; mathematical biology, Warwick)
• £10M MRC programme in multidisciplinary approaches to mental health and neurodegenerative diseases
• BBSRC initiative in predictive/systems biology
6. Self-reflection: Lessons for the UK• Need to involve many different agencies, funding
bodies (Wellcome Trust?)• Need to link into existing schemes which have
strong neuroinformatics components• Need to profit from current UK interest in bringing
together life scientists and “physical” scientists• Need to examine teaching provision
But the infrastructure to develop
UK neuroinformatics is in place!
Nature, 427, 275 (22 January 2004)
Ministers prepare to back neuroscience network
[PARIS] Brain scientists around the world wrestling with the thorny problem of how to share their data should soon find their lives getting a little easier.
Plans for an international facility to integrate such information are expected to be endorsed next week at a meeting in Paris of 30 science ministers from countries in the Organisation for Economic Co-operation and Development (OECD).
The planned International Neuroinformatics Coordinating Facility would bring together disparate neuroscience databases to allow researchers to share and compare their results more readily (see Nature, 406, 822-825; 2000).
The facility would build its own databases, nurture agreements between nations on data sharing, and even fund some research on neuroinformatics, says Stefan Michalowski, executive secretary of the OECD’s Global Science Forum. The annual cost of the administrative body that would run the facility would be about US$1.2 million.