The Information Environment for Neuroscientists

1. The Information Environment for Neuroscientists David R Newman (drn@ecs.soton.ac.uk)

2. Overview • Introduction • What is NeuroHub about? • Some related projects • How does this fit together? • What we WON’T Do • Questions

3. Introduction • Project between Oxford, Southampton and Reading Universities • Oxford • Nigel Emptage’s Lab • Southampton • Vincent O’Connor’s Lab • Phil Newland’s Lab

4. What is NeuroHub All About? Making Neuroscientists’ Lives Easier!!!

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

6. How? • Conversion of File Formats • Consistent Annotation Method • Web-based Repository for Data • Search Interfaces • For Images • For Videos • For Data • Collaborative Document Editing • Blog Interface • Literature Sharing File Space

7. Jam Today, Jam Tomorrow Thursday’s Jam Friday’s Jam

8. Related Projects

9. 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 devices • Automatically from electronic devices • Otherwise manually (scanned / typed in) • Creates a visual and easy readable record of experiments

10. “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”

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

12. Research Information Centre (RIC) • Extends Microsoft SharePoint • [EXPLANATION] • Web-based system • Manage research projects • Support scientific collaboration

13. 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

14. Semantic Web Applications in Neuromedicine (SWAN) • Organize & annotate scientific knowledge about neurodegenerative disorders • Create tools to manage all this data • Facilitate 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?

15. My Background • Worked as part of the myExperiment team • Involved in the eLab TAG • Have worked with Neuroscientists from the SWAN project • Interested in: • Consistent Data Annotation • Organization of Experimental Data • Using Resource Description Framework (RDF)

16. What is RDF? Subject Object Cows Home Come Predicate Are Is A Animals House

17. How does this impact on NeuroHub? • CombeChem gives insight into what a scientist might find useful • Blog3 / 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

18. Environment Architecture Data Capture Device PC Data Capture Device PC Analysis Server Oxford Southampton SotonEprints ORA Community

19. What We Won’t Do • Will 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

20. What’s Next?

21. Questions ?