1. The Chemtools LaBLog Recording research in the real world Cameron Neylon Contributions from Jeremy Frey, Andrew Milsted, Steve Wilson, Simon Coles, Mark Borkum, Jenny Hale, and others

2. Goals

A complete and useable record for the researcher and research team

Enable a human reader to fully reproduce all experiments and replicate all data analysis in detail

New functionality (video, search, communication, links, visualisation)

Enable machine reading for automated aggregation and analysis

3. A small challenge Can anyone name or identify a paper in which it is possible to completely and precisely replicate the data analysis, including availability of raw data, full details of tools, version, and parameters for data analysis, and version (or date) of any databases used in the analysis. 4. A blog as the lab book http://chemtools.chem.soton.ac.uk/projects/blog / Bio Blogs http://blogs.openwetware.org/scienceintheopen Discussion 5. One item one post (1I-1P) system 6. 1I-1P gives every sample a URI 7. 1I-1P relationships between posts An rdf dump of posts and links between them rendered using Welkin (simile.mit.edu/welkin) 8. 1I-1P relationships between posts 9. What about semantics?

System is semantically unaware

Arbitrary key-value pairs stored as XML

Complete freedom to add or modify metadata

Complete freedom to muck it up

10. Templates provide ease of use and consistent metadata [table] [row] Lane[col]Sample[col]ul [/row] [row] 4[col] [[Dna:%]] [col] [[box]] [/row] [/table] [[Section>Procedure]] [[Procedure_Type>electrophoresis_agarose]] [[Sandpit_group>DrexelDemo]] 11. System to date

Our main laboratory notebook system

Around 4000 posts, 800 Gb of data

Used for biochemistry, synthetic chemistry, biophysics

Also used as a collaboration and management tool in other projects

Currently rolling out onto other sites

12. Goals

A complete and useable record for the researcher and research team

Enable a human reader to fully reproduce all experiments and replicate all data analysis in detail

New functionality (video, search, communication, links, visualisation)

Enable machine reading for automated aggregation and analysis

13. Versioning and provenance for analysis using workflows and API

Workflow enacted online (MyExperiment)

Pull down data from lab book and process

Write results and record back to blog

Provenance of workflow, versioning, and sharing via MyExp

Record of enactment in LaBLog

14. Automatic Blogging by Machines 15. Automatic Blogging by Sensors

Continuous log of environmental conditions in a laboratory

Instant detection of erroneous events

Correlate with inconsistencies in datasets

16. Goals

A complete and useable record for the researcher and research team

Enable a human reader to fully reproduce all experiments and verify all data analysis in detail

New functionality (video, search, communication, links, visualisation)

Enable machine reading for automated aggregation and analysis

17. Visualisations and communication 18. 19. 20. Pictorial commenting

Annotation tools allow comments and foster collaboration and / or communication

Need for more advanced Blog tools / technology around data

21. Goals

A complete and useable record for the researcher and research team

Enable a human reader to fully reproduce all experiments and verify all data analysis in detail

New functionality (video, search, communication, links, visualisation)

Enable machine reading for automated aggregation and analysis

? 22. RDF to real RDF?

Currently just links and post titles

Include metadata

Infer a vocabulary (probably human driven process)

Refactor to generate a rich rdf version

23. Linking it all up Unstructured Unfiltered Arbitrary vocabulary Structured Filtered Controlled vocab Primary lab book Autoblogging instrument Published paper Database entry Personal journal Raw data Data processing 24. What could it look like? GO Ontology Browser Raw SANS Data - D22 run #29483 fromD22 at the Institut Laue-Langevin Raw SANS Data - D22 run #29483 fromD22 at the Institut Laue-Langevin 25.