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The Information The Information Environment for Environment for NeuroscientistsNeuroscientists
David R Newman([email protected])
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OverviewOverviewIntroductionWhat is NeuroHub about?Some related projectsHow does this fit together?What we WON’T DoQuestions
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IntroductionIntroductionProject between Oxford,
Southampton and Reading Universities
Oxford◦Nigel Emptage’s Lab
Southampton◦Vincent O’Connor’s Lab◦Phil Newland’s Lab
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What is NeuroHub All What is NeuroHub All About?About?
Making Neuroscientists’ Lives Easier!!!
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More Specifically...More Specifically......Help Managing Your Data...Help Managing Your Data
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How?How?Conversion of File FormatsConsistent Annotation MethodWeb-based Repository for DataSearch Interfaces
◦ For Images◦ For Videos◦ For Data
Collaborative Document EditingBlog InterfaceLiterature Sharing File Space
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Jam Today, Jam Jam Today, Jam TomorrowTomorrow
Thursday’s Jam Friday’s Jam
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Related ProjectsRelated Projects
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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
Manages outputs from experiment devicesAutomatically from electronic devicesOtherwise manually (scanned / typed in)
Creates a visual and easy readable record of experiments
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“Social networking site for scientists”
Users can:◦Make “friends” and join groups◦Upload and describe experiment-related
files◦Use the social network to share ◦Allow other users to annotate these files◦Collate items into “Packs” and in the
future “Research Objects”
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e-Laboratories Technical e-Laboratories Technical Architecure Group (eLab Architecure Group (eLab TAG)TAG)
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Research Information Centre Research Information Centre (RIC)(RIC)Extends Microsoft SharePoint
◦[EXPLANATION]Web-based system
◦Manage research projects◦Support scientific collaboration
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Focussed around NeurophysiologyVirtual Laboratory Environment through
a Portal for Sharing Data and Programs◦ Annotate uploaded files◦ Search across archived datasets◦ Run analysis over datasets using programs on
CARMEN as well as their computing resourcesPromotes Standards
◦ MINI: Minimum Information about a Neuroscience Investigation
◦ NDTF: Neurophysiology Data Translation Format
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Semantic Web Semantic Web Applications in Applications in Neuromedicine (SWAN)Neuromedicine (SWAN)Organize & annotate scientific
knowledge about neurodegenerative disorders
Create tools to manage all this dataFacilitate the development and testing
of hypotheses◦Do hypotheses agree or disagree?◦What evidence supports or contradicts an
hypothesis?◦What questions are unanswered and how can
hypotheses be created and tested for these?
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My BackgroundMy BackgroundWorked as part of the
myExperiment teamInvolved in the eLab TAGHave worked with Neuroscientists
from the SWAN project Interested in:
◦Consistent Data Annotation◦Organization of Experimental Data◦Using Resource Description Framework
(RDF)
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What is RDF?What is RDF?Subject
Predicate
Object
Come
Animals House
AreIs A
Cows Home
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How does this impact on How does this impact on NeuroHub?NeuroHub?CombeChem gives insight into what a
scientist might find usefulBlog3 / RIC / Research Objects may
provide a basis to help manage data as it moves around the lab
myExperiment provides facility for social curation of data
CARMEN provides standards for consitent data annotation
SWAN could assist on determining what experiments to do next
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Environment ArchitectureEnvironment Architecture
Data Captur
e Device
PC
Data Captur
eDevice
PCAnalysi
s Server
SouthamptonOxford
Community
ORASoton Eprin
ts
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What We Won’t DoWhat We Won’t DoWill not be some large monolithic
system based on a strict inflexible set of user requirements
Will not adversely affect how neuroscientists currently conduct their research
Should not take excessive training to learn how to use
Must not create extra unwanted work for the neuroscientist
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What’s Next?What’s Next?
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Questions ?