An Information Environment for Neuroscientists David Spence Oxford e-Research Centre

Outline Introduction Neuroscience areas The plan Related projects Our current work

Introduction JISC funded project Collaboration between Oxford, Southampton and Reading Universities 4 FTEs, 3 years

The Team Oxford ◦ Anne Trefethen ◦ David Wallom ◦ Steven Young ◦ Neil Caithness ◦ John Pybus ◦ David Spence ◦ Kang Tang ◦ Nigel Emptage Southampton ◦ Dave De Roure ◦ Jeremy Frey ◦ David Newman ◦ Mark Borkum ◦ Philip Newland ◦ Vincent O’Connor Reading ◦ Mark Baker ◦ Garry Smith ◦ Doug Saddy

The Neuroscience: Oxford 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 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 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 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

Challenges Interdisciplinary teams – different expectations, cultures, requirements Agreed standards ◦ 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

Processes Higher-level: research-cycle PIs Lower-level: experimental-cycle All researchers

Making better use of computing technology ◦ SmartTea investigated how chemists experiment ◦ Electronic Lab Notebooks (ELNs)  Useful in some scenarios  Chemists involved still use their logbook s Manages outputs from experiment devices 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 ◦ Annotate uploaded files ◦ Search across archived datasets ◦ Run analysis over datasets using programs on CARMEN as well as their computing resources Promotes Standards ◦ MINI: Minimum Information about a Neuroscience Investigation ◦ NDTF: Neurophysiology Data Translation Format

A Virtual Research Environment for Cancer Imaging (VRE-CI) VRE-CI extends the functionality of RIC ◦ include tools for articulating and sharing imaging algorithms through the integration of Trident Research Information Centre (RIC) ◦ Microsoft/British Library VRE for Bioscientists ◦ Based on Microsoft Sharepoint

Major requirements Data management ◦ 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

What are we doing now? Requirements capture ◦ 4 prototypes  Data sharing and tagging  Digital Pens  File conversion  Metadata ◦ Further interviews Design ◦ “Ideas gathering”  Looking at other projects ◦ Basic design of data system

Environment Architecture Data Capture Device PC Data Capture Device PC Analysis Server SouthamptonOxford Community ORA Soton EPrints myExperiment for supporting interaction within the community Tools on PCs for analysing data Blog3 or similar with additional functionality on the group systems Meta data generation

A projected Neurohub node... File serverBlog3 GLUEGLUE Upload area Download area Annotate/ search Web up/ download Blogging Standard instrument PC Analysis PC Web browser Digital Pens Instrument PC – with tools

Conclusions 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 We want to allow neuroscientists to continue to work in the same way Ease of integration into the neuroscientists working environment

Questions