please tweet - everything! #openashdb @danmaclean - bioinformatics @kamounlab – pathogenomics...
TRANSCRIPT
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• Please tweet - everything!• #openashdb
@danmaclean - bioinformatics
@kamounlab – pathogenomics
Crowdsourcing for ash dieback
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Crowdsourcing for ash dieback
Kentaro Yoshida,Diane Saunders, Sophien Kamoun and Dan MacLean
GMOD meeting 5.April.13
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Ash tree (Fraxinus Excelsior)
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Yggdrasil in Norse mythology is a giant Ash.
"The Ash Yggdrasil" (1886) by Friedrich Wilhelm Heine.
• Healing treePre-Christian: Pass a sick child through split tree: if it resealed the child would be cured.
• Strong Furniture
• Withstand shocks Oars, cues, truncheons, hockey sticks etc
Central in Norse cosmology
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Lesions and cankers on stems/branches
Visible throughout the year
Leaves with brown leaf
stalksThroughout
summer
Fruiting bodies on fallen leaf
stalks Visible from
spring
Ash dieback
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Ash dieback symptoms
Photos: Iben M ThomsenIn Denmark
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Chalara fraxinea
Alias: Hymenoscyphus pseudoalbidus
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Ash dieback disease – Chalara fraxinea
2012
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Ash dieback
http://ashtag.org
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Science is too slow in emergencies
We have to wait for funding of relatively isolated groups
on specific projects
Structure of science inhibits
collaboration and sharing
Publication cycle bad for us
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“many hands make light work”
Crowdsourced analyses, open access data
let the experts at the data
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Crowdsourced analyses “live peer review – the global on-line lab meeting”
Let the experts review the results as they appear – live filtering
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Why crowdsourcing might help
• >3000 people hospitalized
• 50 deaths in Germany
• Outbreak tracked to Fenugreek seeds (used as a herb, spice or vegetable)
Scientific response
Dr Loman joined up sequences
(@pathogenomenick)
24h 48h 72h 96h 120h 144h 168h
DNA-based diagnostics Key findings identified:
• How it kills • Toxin genes
(Example) Applying crowdsourcing to deadly diseases: E. coli outbreak Germany 2011
github: ehec-outbreak-crowdsourced / BGI-data-analysis
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an initiative to fast-forward collaboration on chalara dieback of ash
OpenAshDieBack
http://oadb.tsl.ac.uk
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Data
Which license ?• NONE WHATSOEVER!• NOT Fort Lauderdale, NOT Toronto.• COMPLETELY OPEN ACCESS, PUBLIC DOMAIN!
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github
version management and contribution tracking
pull data
make change
pushback
The data and results themselves are actually hosted externally on the public website, github.
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What the repo is -
• Basically just as directory structure – semantically organized ‘github.com/ash-dieback-crowdsource/data’
• A fork of a generic repo for this stuff ‘github.com/danmaclean/crowdsrc’
you can start your own right now
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Github accessesNumber of signups: 21 Directory size (not including reads): 4.32 GbNumber of commits: 103
Quite a large labgroup So from nothing were generated a whole new research group
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All analyses contributed(what we learnt since December!)
is on the wiki and blog
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a hub for analysis reports
Diane Saunders @ TSLhttp://oadb.tsl.ac.uk
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Look for genes with similarity to known disease causing proteins
C. fraxinea toxin (NLP1)
• Recognized a toxin based on its similarity to a common fungal toxin (toxic to plants)
C. fraxinea NLP1
Fungal NLPIdentical regions in blue
C. fraxinea NLP1
FungalNLP
toxic part of protein
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Getting bioinformaticians is fine, want also to get bench biologists involved
(these know all about pathogen!)need new infrastructure
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OADB
cloud tools
Data Store
Dedicated interim raw data storage
GitHub assembly and annotation hosting (bioinformaticians)
Assembly and annotation web-tool (bench biologists)
Administrative middleware
Hub website and access point
?
G-ny-MOD - ‘Generic not-yet-a Model Organism Database’
Holds data while model under construction
ftp-oadb.tsl.ac.uk
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gee fuportable feature and assembly versioning database
RESTful API – script access
Works well for small groups of biologistsVery small internal tool – not yet ready for primetime, but lightweight
github.com/danmaclean
Dan MacLean
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gee fu - ‘experiments’
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gee fu - ‘tools’
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gee fu - ‘tools’
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gee fu - ‘tools’
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gee fu browsing
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Right now- we’re building this
• But we need a good tool – WebAppollo??
• We ask you now to give us suggestions (we’re crowdsourcing you right now)• We REALLY would like a better solution than
“gee fu”! Let us know! • How can GMOD accommodate these needs!
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http://oadb.tsl.ac.uk
How to get involvedgo and get the data!do your stuff with it!
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Data available now
Data available very soon
1. Infected ash RNA-seq Illumina paired reads
2. Chalara genome sequence and gene annotation
3. Chalara ITS sequence
4. Chalara Calmodulin sequence
Ash genomic DNA Illumina paired reads
..your data?
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Nornex – getting biggerLots of partners now agreeing to provide data and analyses on ash dieback
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What is the next step?
Continue to encourage engagement from experts in the field to help with analyses
Oadb.tsl.ac.uk
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MacLean Bioinformatics group
Dan MacLean@danmacleanGraham Etherington
Kamoun Pathogenomics Group
Sophien Kamoun@kamounlabKentaro YoshidaDiane SaundersSuomeng DongJoe Win
University of ExeterGenepool (Edinburgh)Forest ResearchEast Malling ResearchFood and Environment Research Agency (FERA, York)
The John Innes CentreThe Genome Analysis Centre
University of CopenhagenNorwegian Forest and Landscape Institute
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AND YOU??? Oadb.tsl.ac.uk