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Biodiversity & Citizen Science in the Genomic Era
- 1. Biodiversity & Citizen Science in the genomics era SUJEEVAN RATNASINGHAM
- 2. What is Citizen Science? Engagement ‘Real’ Science Reach
- 4. Modern Citizen Science Data Contribution Resource Contribution Cognitive Contribution CPU time sharing Network Bandwidth Puzzle Solving Pattern Recognition Transcription Image Capture Event Capture
- 5. Citizen Science Tools for Biodiversity
- 6. Data Collected Observation Records Species Observed
- 9. Impact of Access to Technology
- 10. Role of Technology: 23andMe 500K SNPs – Illumina Beadchip Array 77 Peer Reviewed Articles in Top Tier Journals Since 2010 +1 Millions Users To Date
- 11. 23andMe: Some Interesting Data
- 12. 23 and Me: BMI This gene encodes apolipoprotein (apo-) A-2, which is the second most abundant protein of the high density lipoprotein particles. The protein is found in plasma as a monomer, homodimer, or heterodimer with apolipoprotein D. Defects in this gene may result in apolipoprotein A-II deficiency or hypercholesterolemia. -RefSeq, June 2013
- 16. 1000+ Institutions from 94 countries sharing data on BOLD AcrossNations Within Nations 100K+ 10K – 100K 1K – 10K BOLD User Network - 2015
- 17. Collection of Rich Data Specimen IDs Trace Data Geography DNA Sequence Audit Trail Taxonomy Images Specimen Descriptions Primers Mass Chemical Properties Isotopes Ecology Morphology ??? Project Metadata Links
- 18. Barcode Index Number (BIN) Algorithm Registry • Tuned to the marker (COX1) • Fixed parameters for balanced OTU generation • Uses prior threshold but refines for each group • Occurrence of DNA Barcode (place and time) • Aggregation of all associated metadata • Reusable - works across studies
- 19. BOLD:AAF2716 Notioplusia illustratataOraesia Janzen 03 Ctenoplusia sp. ANIC1
- 20. Genomics in Citizen Science Centralized System Distributed System
- 21. Sample to Answer Unidentified Organism Taxon Range Conservation Status Life Cycle Invasive? Behavior Images of Larvae Images of Adults Disease Vectors?
- 24. LifeScanner Barcoding Workflow Species Identification ID Engine Sample Collection Sequencing PCR Prep Partner Sequencing Labs
- 25. Live Updates
- 27. San Diego City Insect Survey 5 km
- 28. Canada Wide Fish Study 300 Volunteers from 180 Cities Surveying 40 Species at 42 Retailers
- 29. Canada Wide Fish Study
- 32. Nanopore Data – Single Sample
- 33. Nanopore Data – Single Sample
- 34. Nanopore based barcodes BOLD:AAC1312 Toxomerus geminatus BOLD:AAB8911 Polydrusus formosus
- 36. Contents (Left to Right): • 1 x Compact quad core GPU accelerated mini –server • 1 x iPhone macro lens • 2 x Pipettes • 1 x iPhone (bring your own) • 1 x 8 channel thermocycler • 20 x LifeScanner v2 kits • 1 x Oxford Nanopore MinION sequencer • 1 x Vortex • 1 x Microcentrifuge
- 38. Future
- 39. Acknowledgements CBG Informatics Team Paul Hebert Dan Janzen & Winnie Hallwachs Torbjorn Ekrem Many others! Canadian Centre for DNA Barcoding CBG Collections Team
Editor's Notes
- Example Zooniverse – Mars crater annotation
- -Sufficiently mature technology
- Add a two sided network – within institute network on top and between institute network on the bottom – metaphor of tip of the iceberg
- Lantana camara (wild sage) – invasive plant although ornamental and historical botanical uses Notioplusia illustrata – native to the Greater Antilles with type locality in st.kitts
- 304 species/bins 41 new species
- We are solving the problems of access and understanding – this creates opportunities in unexpected areas