Scott Edmunds

The
[BBSRC](http://www.bbsrc.ac.uk/home/home.aspx "BBSRC homepage"){target="_blank"
rel="noopener"} has just released an excellent
[video](http://youtu.be/ttMnQIE-P-s "Crowdsourcing video"){target="_blank"
rel="noopener"} and
[article](http://www.bbsrc.ac.uk/news/food-security/2013/130218-f-crowdsourcing-killer-outbreaks.aspx "BBSRC crowdsourcing write-up"){target="_blank"
rel="noopener"} on crowdsourcing killer disease outbreaks very relevant
to our [recent
commentary](http://www.gigasciencejournal.com/content/2/1/2 "OpenAshDB paper"){target="_blank"
rel="noopener"} and [blog
postings](http://blogs.biomedcentral.com/gigablog/2013/02/13/open-science-versus-ash-dieback-and-the-tweenome-revisited/ "Tweenome revisited blog"){target="_blank"
rel="noopener"} on the
[OpenAshDB](http://oadb.tsl.ac.uk/ "OpenAshDB website"){target="_blank"
rel="noopener"} (the Ash Dieback disease crowdsourcing) project.
Featuring interviews from Nick Loman and Lisa Crossman (also an author
on our [OpenAshDB
paper](http://www.gigasciencejournal.com/content/2/1/2 "OpenAshDB paper"){target="_blank"
rel="noopener"}), key contributors to the 2011 *E. coli* O104:H4
outbreak genome crowdsourcing effort, it gives a very good overview of
the how our initial release of public domain genomic
[data](http://dx.doi.org/10.5524/100001 "E. coli DOI"){target="_blank"
rel="noopener"} via twitter helped kick-start a burst of crowd-sourced,
curiosity-driven analyses around the world aimed at understanding and
fighting the outbreak.

We have written a lot about this twitter driven ["tweenome"
analysis](http://blogs.biomedcentral.com/gigablog/2011/08/03/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/ "Notes from a Tweenome blog"){target="_blank"
rel="noopener"} in the past, but this [video and
article](http://www.bbsrc.ac.uk/news/food-security/2013/130218-f-crowdsourcing-killer-outbreaks.aspx "BBSRC crowdsourcing write-up"){target="_blank"
rel="noopener"} tries to learn lessons from the *E. coli* project and
use these experiences for the related effort to tackle the devastating
spread of Ash Dieback disease in Europe. Since the publication of the
[OpenAshDB
paper](http://www.gigasciencejournal.com/content/2/1/2 "OpenAshDB paper"){target="_blank"
rel="noopener"} (currently our [most
viewed](http://www.gigasciencejournal.com/mostviewed "Most viewed articles"){target="_blank"
rel="noopener"} article this month), further analyses and data continues
to be added to the [GitHub based
repository](https://github.com/ash-dieback-crowdsource "AshDieback GitHub"){target="_blank"
rel="noopener"}, including [geospatial
data](https://github.com/ash-dieback-crowdsource/data/tree/master/ash_dieback/chalara_fraxinea/geospatial_data "Geospatial data in GitHub"){target="_blank"
rel="noopener"} and new [secretome
predictions](https://github.com/ash-dieback-crowdsource/data/tree/master/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/annotations/Secretome_prediction "Secretome predictions folder in GitHub"){target="_blank"
rel="noopener"}. The BBSRC is taking a big interest in the potential of
this method of potentially speeding up research practices, with the
[recent
announcement](http://www.bbsrc.ac.uk/funding/opportunities/2013/crowd-sourcing-biological-sciences.aspx "BBSRC crowdsourcing grant"){target="_blank"
rel="noopener"} of funding for up to £2M proposals to develop and deploy
crowdsourcing approaches to complex, large-scale scientific problems.
Further interesting viewing on this subject include Mark Pallen's
[excellent
talks](http://youtu.be/HyN2BZPItrg "Mark Pallen video"){target="_blank"
rel="noopener"} on open-source genomics, and the brilliant [TEDx
talk](http://youtu.be/LmAugMSJ1-Y "Jennifer Gardy on 21st century public health"){target="_blank"
rel="noopener"} by Jennifer Gardy on 21st century public health. This
talk was extremely prescient in 2009, and highlighted early efforts
using [wiki based
resources](http://tree.bio.ed.ac.uk/groups/influenza/ "H1N1 wiki"){target="_blank"
rel="noopener"} for tackling that years H1N1 influenza pandemic.

As the cost of and speed of sequencing continues to drop, these early
examples hopefully will inspire and encourage what our editorial board
member Mike Schatz terms in another recent *GigaScience* commentary: the
rise of a "digital immune system", by observing the microbial landscape,
detecting potential threats, and neutralizing them before they spread
beyond control. The ultimate aim of these projects is to shape the way
we tackle future infectious disease outbreaks, speeding up the response
to such an extent we potentially stop these outbreaks before they even
happen. These are laudable goals and a fantastic example of what can be
enabled by open-science, and
[*GigaScience*](http://www.gigasciencejournal.com/){target="_blank"
rel="noopener"} will continue to do what we can to help promote and
encourage such schemes in the future.

**Further Reading**  
[1.](http://www.gigasciencejournal.com/content/2/1/2 "OpenAshDB paper"){target="_blank"
rel="noopener"} MacLean, D; et al., Crowdsourcing genomic analyses of
ash and ash dieback --- power to the people. *GigaScience* 2013,
**2**:2  
[2.](http://oadb.tsl.ac.uk/ "OpenAshDB website"){target="_blank"
rel="noopener"} OpenAshDB Website:
[http://oadb.tsl.ac.uk/](http://oadb.tsl.ac.uk/ "OpenAshDB website"){target="_blank"
rel="noopener"}  
[3.](http://www.gigasciencejournal.com/content/1/1/4 "Rise of the Virtual Immune System"){target="_blank"
rel="noopener"} Schatz, MC & Phillippy, AM The rise of a digital immune
system. *GigaScience* 2012, **1**:4

The post [Tweenome on Film: Excellent Video on Crowdsourcing Killer
Outbreaks](http://gigasciencejournal.com/blog/tweenome-on-film-excellent-video-on-crowdsourcing-killer-outbreaks/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


The BBSRC has just released an excellent video and article on crowdsourcing killer disease outbreaks very relevant to our recent commentary and blog postings on the OpenAshDB (the Ash Dieback disease crowdsourcing) project.

Tweenome on Film: Excellent Video on Crowdsourcing Killer Outbreaks

![E coli bacteria, as shared as a
tweenome](http://upload.wikimedia.org/wikipedia/commons/8/84/Diverse_e_Coli.png?uselang=en-gb){.alignleft
decoding="async" style="width: 180px; height: 134px;" width="712"
height="514" align="left" border="0" hspace="5" vspace="5"}Last week
marked two important milestones in the deadly 2011 European *E. coli*
0104:H4 outbreak: the Robert Koch institute
[announcing](http://www.rki.de/cln_162/nn_217400/EN/Home/PM__EHEC.html "R Koch"){target="_blank"
rel="noopener"} the end of the outbreak, and the
[publication](http://www.nejm.org/doi/full/10.1056/NEJMoa1107643? "BGI NEJM"){target="_blank"
rel="noopener"} of
[several](http://www.nejm.org/doi/full/10.1056/NEJMoa1106920 "PACBio paper"){target="_blank"
rel="noopener"}
[papers](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022751 "Munster PLoSOne"){target="_blank"
rel="noopener"} from the many groups sequencing the pathogen. This
included a
[publication](http://www.nejm.org/doi/full/10.1056/NEJMoa1107643? "BGI NEJM"){target="_blank"
rel="noopener" wplink-edit="true"} in the New England Journal of
Medicine by groups from the BGI, UMC Hamburg-Eppendorf, and Birmingham
University acknowledging members of the crowdsourcing community and the
work achieved using the genome sequence our colleagues at the BGI made
available via our *GigaScience*
[database](http://dx.doi.org/10.5524/100001 "E coli BGI data"){target="_blank"
rel="noopener"}. This was our first dataset released with a
[DOI](http://en.wikipedia.org/wiki/Digital_object_identifier "Digital Object Identifier"){target="_blank"
rel="noopener"} and under the freest
[CC0](http://en.wikipedia.org/wiki/CC0#Public_domain_tools "CC0"){target="_blank"
rel="noopener"} public domain license, so now is a great opportunity to
look back to see the consequences of this novel form of data release.

Due to the unusual severity of the outbreak -- thousands severely ill
and 50 deaths to date, it was clear that the usual scientific procedure
of producing data, analyzing it slowly and then releasing it to the
public after a potentially long peer-review procedure would have been
unhelpful in this case. By releasing the first genomic data before it
had even finished uploading to
[NCBI](http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Link&LinkName=bioproject_sra&from_uid=67657 "NCBI E coli data"){target="_blank"
rel="noopener"} via
[twitter](http://sciblogs.co.nz/infectious-thoughts/2011/06/09/an-outbreak-of-crowdsourcing/ "An outbreak of crowdsourcing"){target="_blank"
rel="noopener"}, and promoting its use and releasing
[subsequent](http://www.genomics.cn/en/news/show_news?nid=98856 "hybrid assembly"){target="_blank"
rel="noopener"}
[improved](http://www.genomics.cn/en/news/show_news?nid=98867 "final assembly"){target="_blank"
rel="noopener"} assemblies this way, a huge community of microbial
genomicists around the world took up the challenge to study the organism
collaboratively (a process that was
[dubbed](http://twitter.com/#!/pathogenomenick/status/78768010382422016 "tweenome"){target="_blank"
rel="noopener"} by some to have made *E. coli* the first "Tweenome").
Once a
[github](https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki "E. coli github"){target="_blank"
rel="noopener"} repository had been created (thanks to the efforts of
the
[Era7](http://www.era7bioinformatics.com/en/index.html "Era7"){target="_blank"
rel="noopener"} team in Spain) to provide a home to these analyses and
data, groups around the world started producing their own annotations
and
[assemblies](http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/ "Nick Loman assembly"){target="_blank"
rel="noopener"} within 24 hours, and within a couple of a days a
potential ancestral strain had been
[identified](http://scienceblogs.com/mikethemadbiologist/2011/06/i_dont_think_the_german_e_coli.php "Ancestor strain"){target="_blank"
rel="noopener"} (further clearing Spanish farmers of the blame), and the
many antibiotic resistance genes and pathogenic features were much more
clearly understood. By releasing the data under a
[CC0](http://en.wikipedia.org/wiki/CC0#Public_domain_tools "CC0"){target="_blank"
rel="noopener"} license, this allowed truly open-source analysis, and
the [UK
HPA](http://www.hpa-bioinformatics.org.uk/lgp/genomes "HPA data"){target="_blank"
rel="noopener"} and github members [followed
suit](http://bacpathgenomics.wordpress.com/2011/06/13/e-coli-data-released-under-creative-commons-0-license/ "CC0 following suit")
in releasing their work in this way.

Huge progress was achieved in record time, and from this incredibly
speedy work a free diagnostic protocol and free primers were
[distributed](http://www.genomics.cn/en/news/show_news?nid=98968 "Free E coli test"){target="_blank"
rel="noopener"} by the BGI to immediately help tracking the source of
the outbreak. On top of the good feeling and
[positive](http://www.bio-itworld.com/news/06/02/2011/German-teams-BGI-Life-Technologies-Identify-E-coli-strain.html "BIO-IT world"){target="_blank"
rel="noopener"}
[coverage](http://online.wsj.com/article/SB10001424052702304778304576373650243960700.html "WSJ"){target="_blank"
rel="noopener"} obtained by this (despite some inevitable
[disagreement](http://www.nature.com/news/2011/110721/full/news.2011.430.html "Nature news profile"){target="_blank"
rel="noopener"} over credit and what exactly was
[achieved](http://scienceblogs.com/mikethemadbiologist/2011/07/public_data_publishing_priorit.php "public data"){target="_blank"
rel="noopener"}), these novel forms of pre-publication data release did
not prevent the acquisition of more traditional forms of scientific
credit -- publication in prestigious scientific and medical journals.

On top of all of the scientific and public health lessons to be learned,
coming from a journal perspective this makes it a very important example
and test case of how new and faster methods of scientific communication
and data dissemination can still complement and work alongside the
traditional systems. This is particularly clear as the open-source
analysis was
[published](http://www.nejm.org/doi/full/10.1056/NEJMoa1107643? "BGI NEJM")
in the New England of Medicine, a prestigious organ with a nearly 200
year
[history](http://en.wikipedia.org/wiki/New_England_Journal_of_Medicine "NEJM history"){target="_blank"
rel="noopener"}, and founder of the
[Ingelfinger](http://en.wikipedia.org/wiki/Franz_J._Ingelfinger "Ingelfinger"){target="_blank"
rel="noopener"} rule causing
[issues](http://embargowatch.wordpress.com/2011/04/01/faculty-of-1000-strikes-a-blow-against-the-ingelfinger-rule/ "problems with Ingelfinger"){target="_blank"
rel="noopener"} in some (mainly medical) journals regarding certain
pre-publication forms of data release. Maximizing the use of the data by
putting it into the public domain still did not trump scientific
etiquette and convention that allowed those producing the data to be
attributed and take credit. This is a great argument in favour of
open-data, and an important lesson to all scientists worrying about
setting their data free.

As (we think) the first ever citable [data
DOI](http://datacite.org/whycitedata "Why cite data"){target="_blank"
rel="noopener"} released to an unpublished genome, this new form of
intermediate credit (similar to
[microattribution](http://www.gen2phen.org/researcher-identification-primer/incentivesrewards-scientific-contributions "microattribution"){target="_blank"
rel="noopener"}) did not hinder the eventual publication of the genome
analysis paper. We'd like to thank our collaborators in the
[Datacite](http://datacite.org/ "datacite"){target="_blank"
rel="noopener"} and the [British
Library](http://www.bl.uk/datasets "BL datasets"){target="_blank"
rel="noopener"} for their help issuing the DOIs, and hope it provides a
good example for similar data producers and projects to follow. We have
followed this example with the release of additional unpublished
[genomes](http://climb.genomics.org.cn/g10k "G10K datasets"){target="_blank"
rel="noopener"}, and large supplementary datasets associated with
articles in
[*GigaScience*](http://www.gigasciencejournal.com/ "GigaScience journal"){target="_blank"
rel="noopener"} will be given DOIs to make them more trackable and
findable, further showing their interoperability with traditional
scientific articles and forms of data release. This particular disease
outbreak was unusually pathogenic, and the sterling efforts of the
medical community and suffering of those affected should not be
forgotten. Whilst there are still many unanswered
[questions](http://scienceblogs.com/mikethemadbiologist/2011/07/genomics_speed_kills_and_not_i.php "Genomic epidemiology issues")
and huge amounts of work still to be done, many lessons have hopefully
been learned, and (as highlighted here) this project provides an
excellent example for the future on how a more collaborative and
open-form of science can carried out. As *GigaScience* would like to be
a
[forum](http://www.gigasciencejournal.com/about#publication "about gigascience"){target="_blank"
rel="noopener"} for the discussion of these issues, as well as promote
and work with the
[open-science](http://en.wikipedia.org/wiki/Open_research "Open Research"){target="_blank"
rel="noopener"} movement, we strongly hope that this can continue and
grow.

The post [Notes from an E. coli "tweenome" -- lessons learned from our
first data
DOI.](http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


Last week marked two important milestones in the deadly 2011 European
<em>
 E. coli
</em>
0104:H4 outbreak: the Robert Koch institute announcing the end of the outbreak, and the publication of several papers from the many groups sequencing the pathogen.

Messaggi di Rogue Scholar

Tweenome on Film: Excellent Video on Crowdsourcing Killer Outbreaks

Notes from an E. coli “tweenome” – lessons learned from our first data DOI.