An Information Environment for
Neuroscientists
David Spence
Oxford e-Research Centre
Outline
Introduction
 Neuroscience areas
 The plan
 Related projects
 Our current work
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Introduction
JISC funded project
 Collaboration between Oxford,
Southampton and Reading Universities
 4 FTEs, 3 years
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The Team
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Oxford
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Anne Trefethen
David Wallom
Steven Young
Neil Caithness
John Pybus
David Spence
Kang Tang
Nigel Emptage
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Southampton
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Dave De Roure
Jeremy Frey
David Newman
Mark Borkum
Philip Newland
Vincent O’Connor
Reading
◦ Mark Baker
◦ Garry Smith
◦ Doug Saddy
The Neuroscience: Oxford
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The Oxford group is focused on specific issues
such as the study of the molecular basis of
synapse formation, plasticity and the regulation of
neuronal morphology in the normal and diseased
brain. They are examining the mechanisms of an
activity-dependent form of neural plasticity known
as long-term potentiation (LTP).
◦ Electrophysiology (patch/voltage clamp)
◦ Microscopy (florescent, confocal, TIRF)
The Neuroscience: Southampton
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A focus in Southampton is on the integrative
analysis of brain function/dysfunction. Modelling
aspects of this across levels of biological
organization ranging from molecules, cells, tissue,
systems to animal behaviour.
◦ Electrophysiology
◦ Optical Microscopy
The Neuroscience: Reading
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In Reading the focus is on the physiological and
psychological mechanisms underpinning complex
cognitive behaviours, targeting typical and atypical
development and decline in individuals.
◦ Functional MRI
◦ EEG
Our Approach
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To gain insight into what Neuroscientists
do and what they need:
◦ Embed developers in the neuroscience labs
◦ Complete semi-formal interviews
Change ways of working as little as
possible
 Provide solutions which are relevant to all
Neuroscience
 Introduce existing standards where they
exist
 Bring together existing projects
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Challenges
Interdisciplinary teams – different
expectations, cultures, requirements
 Agreed standards
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◦ Data formats
Microscopes (Multiphoton or Confocal)
Live cell flourescent imaging
Electrophysiology recordings
Behavioural data
◦ Meta data standards
Wide variety of tools used in community
 Wide variety of instruments and software
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Processes
Initial
Experimental
Idea
Initial Idea
Publication
Obtaining
funding
Dissemination
Experiment
Higher-level: research-cycle
PIs
Data Analysis
Experimental
Design
Data
Collection
Lower-level: experimental-cycle
All researchers
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Making better use of computing technology
◦ SmartTea investigated how chemists experiment
◦ Electronic Lab Notebooks (ELNs)
 Useful in some scenarios
 Chemists involved still use their logbooks
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Manages outputs from experiment devices
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Automatically from electronic devices
Otherwise manually (scanned / typed in)
Creates a visual and easily readable record of
experiments
Focussed around Neurophysiology
 Virtual Laboratory Environment through a
Portal for Sharing Data and Programs
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◦ Annotate uploaded files
◦ Search across archived datasets
◦ Run analysis over datasets using programs on
CARMEN as well as their computing resources
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Promotes Standards
◦ MINI: Minimum Information about a Neuroscience
Investigation
◦ NDTF: Neurophysiology Data Translation Format
A Virtual Research Environment for
Cancer Imaging (VRE-CI)
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VRE-CI extends the functionality of RIC
◦ include tools for articulating and sharing
imaging algorithms through the integration of
Trident
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Research Information Centre (RIC)
◦ Microsoft/British Library VRE for Bioscientists
◦ Based on Microsoft Sharepoint
Major requirements
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Data management
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Consistent annotation of data (metadata)
A data storage system for within the groups
Linking of associated data
A data sharing system
“Electronic lab-notebooks”
◦ Simple and lightweight
◦ Linked into data
◦ Linked into digital pens
Other requirements
Community sites for groups such as
SONG
 Integration of data capture devices
 File conversion to a common format
 Collaborative document preparation
 Simple lab supplies ordering system
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What are we doing now?
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Requirements
capture
◦ 4 prototypes
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Data sharing and tagging
Digital Pens
File conversion
Metadata
◦ Further interviews
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Design
◦ “Ideas gathering”
 Looking at other
projects
◦ Basic design of data
system
Environment Architecture
Tools on PCs for analysing data
Meta data generation
Data
Capture
Device
ORA
PC
Oxford
Data
Capture
Device
PC
Southampton
Analysis
Server
Soton
EPrints
Blog3 or similar with additional functionality on the group systems
Community
myExperiment for supporting interaction within the community
A projected Neurohub node...
File server
Upload
area
Download
area
Standard
instrument
PC
G
L
U
E
Blog3
Annotate/
search
Blogging
Analysis PC
Instrument
PC – with
tools
Web up/
download
Digital Pens
Web
browser
Conclusions
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Our aim is to develop a lightweight “Neurohub”
that empowers the researchers
 Existing tools and instruments as the spokes
 Data is key: metadata, storage, search, archive
 Linked into persistent experimental records
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We want to allow neuroscientists to continue
to work in the same way
 Ease of integration into the neuroscientists working
environment
Questions