The Information The Information Environment for Environment for NeuroscientistsNeuroscientists

David R Newman(drn@ecs.soton.ac.uk)

OverviewOverviewIntroductionWhat is NeuroHub about?Some related projectsHow does this fit together?What we WON’T DoQuestions

IntroductionIntroductionProject between Oxford,

Southampton and Reading Universities

Oxford◦Nigel Emptage’s Lab

Southampton◦Vincent O’Connor’s Lab◦Phil Newland’s Lab

What is NeuroHub All What is NeuroHub All About?About?

Making Neuroscientists’ Lives Easier!!!

More Specifically...More Specifically......Help Managing Your Data...Help Managing Your Data

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

Jam Today, Jam Jam Today, Jam TomorrowTomorrow

Thursday’s Jam Friday’s Jam

Related ProjectsRelated Projects

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

“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”

e-Laboratories Technical e-Laboratories Technical Architecure Group (eLab Architecure Group (eLab TAG)TAG)

Research Information Centre Research Information Centre (RIC)(RIC)Extends Microsoft SharePoint

◦[EXPLANATION]Web-based system

◦Manage research projects◦Support scientific collaboration

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

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?

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)

What is RDF?What is RDF?Subject

Predicate

Object

Come

Animals House

AreIs A

Cows Home

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

Environment ArchitectureEnvironment Architecture

Data Captur

e Device

PC

Data Captur

eDevice

PCAnalysi

s Server

SouthamptonOxford

Community

ORASoton Eprin

ts

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

What’s Next?What’s Next?

Questions ?