What can Bioinformaticians
learn from YouTube?

Data

New project. New schema.

EMBL: 20 different data
formats

“A biologist would rather share their
toothbrush than their (gene) names”
Mike Ashburner

YouTube loves to share

100 million views per day

114 apps

<rdf:RDF xmlns=\"http://www.affymetrix.com/community/
publications/affymetrix/tmsplice#\"

<Gene rdf:about=\"#1110002A21Rik\">
<chr>chr1</chr>
<hasVariant rdf:parseType=\"Resource\">
<representedBy rdf:resource=\"#gi13385627\"/>
</hasVariant>
<hasVariant rdf:parseType=\"Resource\">
<representedBy rdf:resource=\"#gi18043402\"/>
</hasVariant>
<strand>+</strand>
</Gene>

RDF, OWL,
SPARQL, GRDDL, WTF?

Lower case ‘s’, lower case ‘w’
The semantic web, not
The Semantic Web

<tr>
<th class=\"two-column\">Gene</th>
<td class=\"two-column\"><table width=\"100%\" cellpadding=\"4\">
<tr>
<td><strong>
<a href=\"http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/
get_data.pl?hgnc_id=1101\">BRCA2</a></div></strong> (HGNC Symbol)
</td>
<td>
<span class=\"small\"> To view all Ensembl genes linked to the name
<a href=\"/Homo_sapiens/featureview?type=Gene;id=BRCA2\">click
here</a>.</span>
</td>
</tr>
</table><p>
This gene is a member of the Human CCDS set: <a href=\"http://
www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?
REQUEST=CCDS&amp;DATA=CCDS9344\">CCDS9344</a>
</p>
</td>
</tr>

<tr class=\"hgene\">
<th class=\"two-column\">Gene</th>
<td class=\"two-column\"><table width=\"100%\" cellpadding=\"4\">
<tr>
<td><strong>
<a href=\"http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/
get_data.pl?hgnc_id=1101\" rel=\"hgnc_name\">BRCA2</a></div></strong>
(HGNC Symbol)
</td>
<td>
<span class=\"small\"> To view all Ensembl genes linked to the name
<a href=\"/Homo_sapiens/featureview?type=Gene;id=BRCA2\"
rel=\"gene_list\" >click here</a>.</span>
</td>
</tr>
</table><p>
This gene is a member of the Human CCDS set: <a href=\"http://
www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?
REQUEST=CCDS&amp;DATA=CCDS9344\" rel=\"ccds\">CCDS9344</a>
</p>
</td>
</tr>

Can our web site
be our API?

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
my $gene = fetch_by_gene_stable_id( 'ENSG00000139618' );

More data on our sites
than through the API
(we’re not the only ones)

RSS

iCal

XML

ational state
Represent
transfer
RESTful service

psd-production/projects

GET
psd-production/projects
RETRIEVE

<projects>
<project>
<id type=\"integer\">8</id>
<created-at type=\"datetime\">2007-10-22T09:43:30+01:00</created-at>
<family-id type=\"integer\">3</family-id>
<name>Test BAC</name>
<updated-at type=\"datetime\">2007-10-22T09:43:30+01:00</updated-at>
<user-id type=\"integer\">1</user-id>
<workspace-id type=\"integer\"/>
</project>
</projects>

POST
psd-production/projects
CREATE

http://psd-production/projects/67

http://psd-production/projects/67

POST
http://psd-production/projects/67
UPDATE

DELETE
http://psd-production/projects/67
DESTROY

No installation
No setup
No fancy protocols

All you need is curl

Perl API

Ruby API

Tools

ows
rkfl
Wo
Tools

It’s all about the workflow

Trace archive vs SSAHA

Workflows are memes
Users add val
ue

YouTube knows memes

Not invented here!

Reproducibility

Go with the flow

Quickly define workflows

Quickly reuse services

Data
Explore
Service Service
Data

Reuse workflows

YouTube for workflows
+
Yahoo! Pipes for
biological data
=
Never having to write
another BLAST parser

Design

Stop hacking

Program to interfaces

“The interface is a contract
between data provider and
data consumer”
Lincoln Stein

Design for reuse

Code for maintenance

Foster “accidental
development”
114 YouTube apps

However...

Designing for reuse is hard

With great power comes
great responsibility

With great power comes
great responsibility
Available Reliable
Accessible

Discoverable:
where is your web site?

Design is for humans

YouTube is ‘only’ an
online video site

A good UI outweighs
smart features

“Monolithic solutions
always fail”
Graham Cameron

Loose coupling rules

Don’t reinvent Eclipse

Thank you

GREENISGOOD.CO.UK