Design Patterns for Lab Experiments

1. Design Patterns for Lab Experiments Cameron McLean PhD Candidate LISC2013 Mark Gahegan FabianaKubke @cammerschooner #labpatterns Centre for eResearch The University of Auckland

3. “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose (Sigma), in a glass-bottomed dish, filled with 0.3% Danieau's solution containing 0.01 mg/ml Tricaine.” Feng Y, Santoriello C, Mione M, Hurlstone A, Martin P (2010) Live Imaging of Innate Immune Cell Sensing of Transformed Cells in Zebrafish Larvae: Parallels between Tumor Initiation and Wound Inflammation. PLoSBiol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

4. “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose(Sigma), in a glass-bottomed dish, filled with 0.3% Danieau's solution containing 0.01 mg/ml Tricaine.” Feng Y, Santoriello C, Mione M, Hurlstone A, Martin P (2010) Live Imaging of Innate Immune Cell Sensing of Transformed Cells in Zebrafish Larvae: Parallels between Tumor Initiation and Wound Inflammation. PLoSBiol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

5. “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose(Sigma), in a glass-bottomed dish, filled with 0.3% Danieau's solution containing 0.01 mg/ml Tricaine.” Feng Y, Santoriello C, Mione M, Hurlstone A, Martin P (2010) Live Imaging of Innate Immune Cell Sensing of Transformed Cells in Zebrafish Larvae: Parallels between Tumor Initiation and Wound Inflammation. PLoSBiol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

6. “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose(Sigma), in a glass-bottomed dish, filled with 0.3% Danieau's solution containing 0.01 mg/ml Tricaine.” Feng Y, Santoriello C, Mione M, Hurlstone A, Martin P (2010) Live Imaging of Innate Immune Cell Sensing of Transformed Cells in Zebrafish Larvae: Parallels between Tumor Initiation and Wound Inflammation. PLoSBiol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

7. @dr_leigh‘s #OverlyHonestMethods

8. Obtaining Lab Protocols @ www.

9. Recording and Representation Σ </>

10. Linked Lab Science

11. Ontological View “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose (Sigma), in a glass-bottomed dish, filled with 0.3% Danieau's solution containing 0.01 mg/ml Tricaine.”

12. Ontological View imaging • diagnostic procedure • subClass Technology-type (JERM) agarose • material chemical polysaccaride • (various OBO) tricane • aminobenzoicanesthetic agent • (NCI thesaurus) NCBO annotator http://bioportal.bioontology.org/annotator

13. Workflows “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose (Sigma), in a glass-bottomed dish, filled with 0.3%Danieau's solution containing 0.01 mg/ml Tricaine.” Agarose Glass Dish Fill Danieau’s Tricane Mount Larvae `

14. An alternate view Forces Σ </>

15. Rather than look to the requirements of the thing, look for the requirements in the environment. The two views are complimentary This is the notion of Christopher Alexander's Design Patterns.

16. We can specify meaning through shared context.

17. Patterns are a design language that document solutions to recurring problems within a specified context Problem… Solution… Context… Forces…

18. Patterns everywhere Forces?

19. Patterns are a design language that document solutions to recurring problems within a specified context

20. Patterns are a design language that document solutions to recurring problems within a specified context N

21. And so, in a laboratory setting - certain problems reoccur…

22. Context: We are using living organisms to understand complex biological processes in their natural setting.

23. Problem: We want to measure and locate a biological entity or process within living cells or a model small animal system.

24. Solution: Couple the process or entity to a light emitting system and detector to enable harmless realtimevisualization and detection.

25. Forces Light Generation Viable Light Detection Immobile Time Matched Transmission

26. “For all of our live imaging studies, larvae were mounted on their sides in 1.5% low melting agarose (Sigma), in a glass-bottomed dish, filled with 0.3% Danieau's solution containing 0.01 mg/ml Tricaine.”

27. Using patterns makes explicit the design rationale

29. So how do we get patterns?

30. Lab patterns for linked science

31. A pattern schema dc:creator Pattern contextDescription { solutionDescription skos:Concept Force skos:definition foaf:depiction Pattern Author vivo:orcidID foaf:Person

32. From paper to RDF

33. OntoWiki Agile Knowledge Engineering and Semantic Web (AKSW) University of Leipzig http://aksw.org/Projects/OntoWiki.html

40. Knowledge elicitation technique Fill a gap in our science record LOD vocabulary and informational resource for experiment design Complement additional representations

41. “We bump into a world of objects and processes, of properties and relations, but we bump into them via the background theory, facts, and values that all shape what count as the sorts of things we bump into.” David Boersema

42. Thanks! Contact me if you are a lab person and want to share your knowledge… @cammerschooner ca.mclean@auckland.ac.nz Acknowledgements Prof Mark Gahegan DrFabianaKubke DrSiouxsie Wiles CeR folks Pictograms from The Noun Project Pencil – Korokoro Gap – Luis Prado Rat- Timothy Dilich Think – James Fenton Arrow - P.J. Onori Puzzle – Javier Cabezas Light bulb - Chris Brunskill Cell- Maurizio Fusillo Transmission -Anna Donlin Surveillance - MarwaBoukarim

43. References Wolstencroft, K., Owen, S., Horridge, M., Jupp, S., Krebs, O., Snoep, J., et al. (2012). Stealthy annotation of experimental biology by spreadsheets. (C. Remick, J. Hunt, H. Javid, L. Bougé, & C. Lengauer, Eds.)Concurrency and Computation: Practice and Experience, 25(4), 467–480. doi:10.1002/cpe.2941 Frey, J. G., Milsted, A., Michaelides, D., & Roure, D. D. (2012). MyExperimentalScience, extending the “workflow.” (C. Remick, J. Hunt, H. Javid, L. Bougé, & C. Lengauer, Eds.)Concurrency and Computation: Practice and Experience, 25(4), 481–496. doi:10.1002/cpe.2922 Milsted, A. J., Hale, J. R., Frey, J. G., & Neylon, C. (2013). LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory. (N. R. Smalheiser, Ed.)PLoS ONE, 8(7), e67460. doi:10.1371/journal.pone.0067460.s007 Castro, L. J. G., McLaughlin, C., & Garcia, A. (2013). Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to the Web of Data. Journal of Biomedical Semantics, 4(Suppl 1), S5. doi:10.1186/2041-1480-4-S1-S5 Heino, N., Tramp, S., & Auer, S. (n.d.). Managing Web Content Using Linked Data Principles - Combining Semantic Structure with Dynamic Content Syndication (pp. 245–250). Presented at the 2011 IEEE 35th Annual Computer Software and Applications Conference - COMPSAC 2011, IEEE. doi:10.1109/COMPSAC.2011.39 Brinkman, R. R., Courtot, M., Derom, D., Fostel, J. M., He, Y., Lord, P., et al. (2010). Modeling biomedical experimental processes with OBI, 1–11. doi:10.1186/2041-1480-1-S1-S7 Klingström, T., Soldatova, L., Stevens, R., Roos, T. E., Swertz, M. A., Müller, K. M., et al. (2013). Workshop on laboratory protocol standards for the molecular methods database. New BIOTECHNOLOGY, 30(2), 109–113. doi:10.1016/j.nbt.2012.05.019 Grassi, M., Morbidoni, C., Nucci, M., Fonda, S., & Ledda, G. (2012). Pundit: Semantically Structured Annotations for Web Contents and Digital Libraries., 49–60. Maccagnan, A., Riva, M., Feltrin, E., Simionati, B., Vardanega, T., Valle, G., & Cannata, N. (2010). Combining ontologies and workflows to design formal protocols for biological laboratories. Automated experimentation, 2, 3. doi:10.1186/1759-4499-2-3 Nonaka, I. (1995). The Knowledge-Creating Company: How Japanese Companies Create the Dynamics of Innovation: How Japanese Companies Create the Dynamics of Innovation. Oxford university press. Singer, R. (2010) Desiging with force. How to apply Christopher Alexander in everyday work. http://vimeo.com/10875362 Boersema, D. (2003). Peirce on explanation. The Journal of Speculative Philosophy, 17(3), 224–236.

45. v1.0 v2.0 Stable “release” snapshots for general consumption A KB of web resources annotated with pattern Concepts. Pattern data wiki free to evolve ?