design patterns for lab experiments
DESCRIPTION
Design Patterns for Lab Experiments. Cameron McLean . PhD Candidate. LISC2013. Mark Gahegan Fabiana Kubke. @ cammerschooner # labpatterns. Centre for eResearch. The University of Auckland. - PowerPoint PPT PresentationTRANSCRIPT
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
</> Σ
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 [email protected]
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
?