1 / 39

Please tweet - everything! # openashdb

Please tweet - everything! # openashdb. @ kamounlab – pathogenomics. @ danmaclean - bioinformatics. Crowdsourcing for ash dieback. Crowdsourcing for ash dieback. Kentaro Yoshida , Diane Saunders, Sophien Kamoun and Dan MacLean GMOD meeting 5.April.13.

nassor
Download Presentation

Please tweet - everything! # openashdb

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Please tweet - everything! • #openashdb @kamounlab – pathogenomics @danmaclean - bioinformatics Crowdsourcing for ash dieback

  2. Crowdsourcing for ash dieback Kentaro Yoshida, Diane Saunders, Sophien Kamoun and Dan MacLean GMOD meeting 5.April.13

  3. Ash tree (Fraxinus Excelsior)

  4. Yggdrasil in Norse mythology is a giant Ash. Central in Norse cosmology • Healing tree • Pre-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 "The Ash Yggdrasil" (1886) by Friedrich Wilhelm Heine.

  5. Ash dieback Leaves with brown leaf stalks Throughout summer Fruiting bodies on fallen leaf stalks Visible from spring Lesions and cankers on stems/branches Visible throughout the year

  6. Ash dieback symptoms Photos: Iben M Thomsen In Denmark

  7. Chalarafraxinea Alias:Hymenoscyphuspseudoalbidus

  8. Ash dieback disease – Chalarafraxinea 2012

  9. Ash dieback http://ashtag.org

  10. We have to wait for funding of relatively isolated groups on specific projects Science is too slow in emergencies Publication cycle bad for us Structure of science inhibits collaboration and sharing

  11. “many hands make light work” Crowdsourced analyses, open access data let the experts at the data

  12. “live peer review – the global on-line lab meeting” Let the experts review the results as they appear – live filtering Crowdsourced analyses

  13. Why crowdsourcing might help (Example) Applying crowdsourcing to deadly diseases: E. coli outbreak Germany 2011 • >3000 people hospitalized • 50 deaths in Germany • Outbreak tracked to Fenugreek seeds (used as a herb, spice or vegetable) Scientific response DrLoman joined up sequences (@pathogenomenick) DNA-based diagnostics • Key findings identified: • How it kills • Toxin genes 168h 144h 48h 72h 96h 120h 24h github: ehec-outbreak-crowdsourced / BGI-data-analysis

  14. an initiative to fast-forward collaboration on chalara dieback of ash OpenAshDieBack http://oadb.tsl.ac.uk

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

  16. The data and results themselves are actually hosted externally on the public website, github. version management and contribution tracking github pull data make change push back

  17. 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

  18. Github accesses Number of signups: 21 Directory size (not including reads): 4.32 Gb Number of commits: 103 Quite a large labgroup So from nothing were generated a whole new research group

  19. All analyses contributed(what we learnt since December!) is on the wiki and blog

  20. a hub for analysis reports Diane Saunders @ TSL http://oadb.tsl.ac.uk

  21. Look for genes with similarity to known disease causing proteins • C. fraxineatoxin (NLP1) • Recognized a toxin based on its similarity to a common fungal toxin (toxic to plants) C. fraxineaNLP1 Fungal NLP Identical regions in blue toxic part of protein Fungal NLP C. fraxinea NLP1

  22. Getting bioinformaticians is fine, want also to get bench biologists involved (these know all about pathogen!)need new infrastructure

  23. G-ny-MOD - ‘Generic not-yet-a Model Organism Database’ Holds data while model under construction GitHub assembly and annotation hosting (bioinformaticians) Data Store cloud tools Dedicated interim raw data storage ftp-oadb.tsl.ac.uk ? Administrative middleware Assembly and annotation web-tool (bench biologists) OADB Hub website and access point

  24. geefu portable feature and assembly versioning database RESTful API – script access Works well for small groups of biologists Very small internal tool – not yet ready for primetime, but lightweight Dan MacLean github.com/danmaclean

  25. geefu - ‘experiments’

  26. geefu - ‘tools’

  27. geefu - ‘tools’

  28. geefu - ‘tools’

  29. geefubrowsing

  30. 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!

  31. How to get involved go and get the data! do your stuff with it! http://oadb.tsl.ac.uk

  32. Infected ash RNA-seq Illumina paired reads Chalara genome sequence and gene annotation Chalara ITS sequence ChalaraCalmodulin sequence Data available now Data available very soon Ash genomic DNA Illumina paired reads ..your data?

  33. Nornex – getting bigger Lots of partners now agreeing to provide data and analyses on ash dieback

  34. What is the next step? Continue to encourage engagement from experts in the field to help with analyses Oadb.tsl.ac.uk

  35. KamounPathogenomics Group SophienKamoun @kamounlab Kentaro Yoshida Diane Saunders Suomeng Dong Joe Win MacLean Bioinformatics group Dan MacLean @danmaclean Graham Etherington University of Exeter Genepool (Edinburgh) Forest Research East Malling Research Food and Environment Research Agency (FERA, York) The John Innes Centre The Genome Analysis Centre University of Copenhagen Norwegian Forest and Landscape Institute

  36. And you??? Oadb.tsl.ac.uk

More Related