Design Patterns for Lab Experiments

@cammerschooner#labpatterns

Centre for eResearchThe University of Auckland

LISC2013Cameron McLean PhD Candidate

Mark GaheganFabiana Kubke

“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. PLoS Biol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

“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. PLoS Biol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

“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. PLoS Biol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

“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. PLoS Biol 8(12): e1000562. doi:10.1371/journal.pbio.1000562

@dr_leigh ‘s#OverlyHonestMethods

Obtaining Lab Protocols

@www.

Recording and

Representation

</>Σ

Linked Lab Science

“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.”

Ontological View

Ontological View- diagnostic procedure subClass Technology-type (JERM)

NCBO annotator http://bioportal.bioontology.org/annotator

- material chemical polysaccaride (various OBO)

- aminobenzoic anesthetic agent (NCI thesaurus)

imaging

agarose

tricane

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.”

Larvae Mount`

Agarose

Danieau’s

Tricane

Glass DishFill

An alternate view

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Forces

Rather than look to the requirements of

the thing, look for the requirements in the

environment. The two views are

complimentaryThis is the notion of Christopher Alexander's Design Patterns.

We can specify meaning through shared context.

Patterns are a design languagethat document

solutions to recurring

problems within a specified context

Problem…Solution… Context…Forces…

Patterns everywhere

Forces?

Patterns are a design languagethat document solutions to recurring problems within a specified context

Patterns are a design languagethat document solutions to recurring problems within a specified context

N

And so, in a laboratory

setting - certain

problems reoccur…

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

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

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

ForcesViable

ImmobileTime Matched

Light GenerationLight DetectionTransmission

“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.”

Using patterns makes explicit the design rationale

So how do we get

patterns?

Lab patterns for linked science

A pattern schema

Pattern

Force

Pattern Author

skos:Concept

foaf:Person

{contextDescriptionsolutionDescriptionskos:definitionfoaf:depiction

dc:creator

vivo:orcidID

From paper to RDF

OntoWiki

http://aksw.org/Projects/OntoWiki.html

Agile Knowledge Engineering

and Semantic Web (AKSW)University of Leipzig

Knowledge elicitation technique

Fill a gap in our science record

LOD vocabulary and informational resource for experiment designComplement additional representations

“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

Thanks!Contact me if you are a lab person and want to share your knowledge…@cammerschooner ca.mclean@auckland.ac.nz

AcknowledgementsPictograms from The Noun ProjectProf Mark

GaheganDr Fabiana KubkeDr Siouxsie WilesCeR folks

Pencil – Korokoro Gap – Luis PradoRat- Timothy Dilich Think – James FentonArrow - P.J. Onori Puzzle – Javier CabezasLight bulb - Chris Brunskill Cell- Maurizio FusilloTransmission -Anna DonlinSurveillance - Marwa Boukarim

ReferencesWolstencroft, 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.

Pattern data wikifree to evolve

Stable “release”snapshots for general consumption

A KB of web resourcesannotated with patternConcepts.

v1.0

v2.0

?