The Chemtools LaBLog Recording research in the real world Cameron Neylon Contributions from Jeremy Frey, Andrew Milsted, S...
Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader t...
A small challenge… Can anyone name or identify a paper in which it is possible to completely and precisely replicate the d...
A blog as the lab book http://chemtools.chem.soton.ac.uk/projects/blog /   “Bio Blogs” http://blogs.openwetware.org/scienc...
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? <ul><li>System is semantically unaware </li></ul><ul><li>Arbitrary key-value pairs stored as XML </l...
Templates provide ease of use and consistent metadata [table] [row] Lane[col]Sample[col]ul [/row] … [row] 4[col] [[Dna:%]]...
System to date <ul><li>Our main laboratory notebook system </li></ul><ul><li>Around 4000 posts, 800 Gb of data </li></ul><...
Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader t...
Versioning and provenance for analysis using workflows and API <ul><li>Workflow enacted online (MyExperiment) </li></ul><u...
Automatic Blogging by Machines
Automatic Blogging by Sensors <ul><li>Continuous log of ‘environmental’ conditions in a laboratory </li></ul><ul><li>Insta...
Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader t...
Visualisations and communication
 
 
Pictorial commenting <ul><li>Annotation tools allow comments and foster collaboration and / or communication  </li></ul><u...
Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader t...
RDF to ‘real’ RDF? <ul><li>Currently just links and post titles </li></ul><ul><li>Include metadata </li></ul><ul><li>Infer...
Linking it all up Unstructured Unfiltered Arbitrary vocabulary Structured Filtered Controlled vocab Primary lab book Autob...
What could it look like? GO Ontology Browser Raw SANS Data - D22 run #29483 from  D22 at the Institut Laue-Langevin Raw SA...
 
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The Chemtools LaBLog

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Presentation on the Chemtools LaBLog electronic notebook system and how I think it could fit into a larger ecosystem of tools and services.

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The Chemtools LaBLog

  1. 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. 2. Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader to fully reproduce all experiments and replicate all data analysis in detail </li></ul><ul><li>New functionality (video, search, communication, links, visualisation) </li></ul><ul><li>Enable machine reading for automated aggregation and analysis </li></ul>
  3. 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. 4. A blog as the lab book http://chemtools.chem.soton.ac.uk/projects/blog / “Bio Blogs” http://blogs.openwetware.org/scienceintheopen Discussion
  5. 5. One item – one post (1I-1P) system
  6. 6. 1I-1P gives every sample a URI
  7. 7. 1I-1P relationships between posts An rdf dump of posts and links between them rendered using Welkin (simile.mit.edu/welkin)
  8. 8. 1I-1P relationships between posts
  9. 9. What about semantics? <ul><li>System is semantically unaware </li></ul><ul><li>Arbitrary key-value pairs stored as XML </li></ul><ul><li>Complete freedom to add or modify metadata </li></ul><ul><li>Complete freedom to muck it up </li></ul>
  10. 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. 11. System to date <ul><li>Our main laboratory notebook system </li></ul><ul><li>Around 4000 posts, 800 Gb of data </li></ul><ul><li>Used for biochemistry, synthetic chemistry, biophysics </li></ul><ul><li>Also used as a collaboration and management tool in other projects </li></ul><ul><li>Currently rolling out onto other sites </li></ul>
  12. 12. Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader to fully reproduce all experiments and replicate all data analysis in detail </li></ul><ul><li>New functionality (video, search, communication, links, visualisation) </li></ul><ul><li>Enable machine reading for automated aggregation and analysis </li></ul>
  13. 13. Versioning and provenance for analysis using workflows and API <ul><li>Workflow enacted online (MyExperiment) </li></ul><ul><li>Pull down data from lab book and process </li></ul><ul><li>Write results and record back to blog </li></ul><ul><li>Provenance of workflow, versioning, and sharing via MyExp </li></ul><ul><li>Record of enactment in LaBLog </li></ul>
  14. 14. Automatic Blogging by Machines
  15. 15. Automatic Blogging by Sensors <ul><li>Continuous log of ‘environmental’ conditions in a laboratory </li></ul><ul><li>Instant detection of erroneous events </li></ul><ul><li>Correlate with inconsistencies in datasets </li></ul>
  16. 16. Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader to fully reproduce all experiments and verify all data analysis in detail </li></ul><ul><li>New functionality (video, search, communication, links, visualisation) </li></ul><ul><li>Enable machine reading for automated aggregation and analysis </li></ul>
  17. 17. Visualisations and communication
  18. 20. Pictorial commenting <ul><li>Annotation tools allow comments and foster collaboration and / or communication </li></ul><ul><li>Need for more advanced Blog tools / technology around data </li></ul>
  19. 21. Goals <ul><li>A complete and useable record for the researcher and research team </li></ul><ul><li>Enable a human reader to fully reproduce all experiments and verify all data analysis in detail </li></ul><ul><li>New functionality (video, search, communication, links, visualisation) </li></ul><ul><li>Enable machine reading for automated aggregation and analysis </li></ul>?
  20. 22. RDF to ‘real’ RDF? <ul><li>Currently just links and post titles </li></ul><ul><li>Include metadata </li></ul><ul><li>Infer a vocabulary (probably human driven process) </li></ul><ul><li>Refactor to generate a rich rdf version </li></ul>
  21. 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
  22. 24. 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
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