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

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

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

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.

A blog as the lab book http://chemtools.chem.soton.ac.uk/projects/blog / “Bio Blogs” http://blogs.openwetware.org/scienceintheopen Discussion

One item – one post (1I-1P) system

1I-1P gives every sample a URI

1I-1P relationships between posts An rdf dump of posts and links between them rendered using Welkin (simile.mit.edu/welkin)

1I-1P relationships between posts

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

System is semantically unaware

Arbitrary key-value pairs stored as XML

Complete freedom to add or modify metadata

Complete freedom to muck it up

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]]

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

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

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

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

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

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

Automatic Blogging by Machines

Automatic Blogging by Sensors Continuous log of ‘environmental’ conditions in a laboratory Instant detection of erroneous events Correlate with inconsistencies in datasets

Continuous log of ‘environmental’ conditions in a laboratory

Instant detection of erroneous events

Correlate with inconsistencies in datasets

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

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

Visualisations and communication

Pictorial commenting Annotation tools allow comments and foster collaboration and / or communication Need for more advanced Blog tools / technology around data

Annotation tools allow comments and foster collaboration and / or communication

Need for more advanced Blog tools / technology around data

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 ?

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

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

Currently just links and post titles

Include metadata

Infer a vocabulary (probably human driven process)

Refactor to generate a rich rdf version

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

What could it look like? GO Ontology Browser Raw SANS Data - D22 run #29483 from D22 at the Institut Laue-Langevin Raw SANS Data - D22 run #29483 from D22 at the Institut Laue-Langevin