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@danmaclean - bioinformatics

@kamounlab – pathogenomics

Crowdsourcing for ash dieback

Crowdsourcing for ash dieback

Kentaro Yoshida,Diane Saunders, Sophien Kamoun and Dan MacLean

GMOD meeting 5.April.13

Ash tree (Fraxinus Excelsior)

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

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

Ash dieback symptoms

Photos: Iben M ThomsenIn Denmark

Chalara fraxinea

Alias: Hymenoscyphus pseudoalbidus

Ash dieback disease – Chalara fraxinea

2012

Ash dieback

http://ashtag.org

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

“many hands make light work”

Crowdsourced analyses, open access data

let the experts at the data

Crowdsourced analyses “live peer review – the global on-line lab meeting”

Let the experts review the results as they appear – live filtering

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

an initiative to fast-forward collaboration on chalara dieback of ash

OpenAshDieBack

http://oadb.tsl.ac.uk

Data

Which license ?• NONE WHATSOEVER!• NOT Fort Lauderdale, NOT Toronto.• COMPLETELY OPEN ACCESS, PUBLIC DOMAIN!

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.

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

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

All analyses contributed(what we learnt since December!)

is on the wiki and blog

a hub for analysis reports

Diane Saunders @ TSLhttp://oadb.tsl.ac.uk

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

Getting bioinformaticians is fine, want also to get bench biologists involved

(these know all about pathogen!)need new infrastructure

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

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

gee fu - ‘experiments’

gee fu - ‘tools’

gee fu - ‘tools’

gee fu - ‘tools’

gee fu browsing

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!

http://oadb.tsl.ac.uk

How to get involvedgo and get the data!do your stuff with it!

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?

Nornex – getting biggerLots of partners now agreeing to provide data and analyses on ash dieback

What is the next step?

Continue to encourage engagement from experts in the field to help with analyses

Oadb.tsl.ac.uk

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

AND YOU??? Oadb.tsl.ac.uk