What can Bioinformaticians learn from YouTube?
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Transcript of What can Bioinformaticians learn from YouTube?
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What can Bioinformaticians learn from YouTube?
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Data
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New project. New schema.
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EMBL: 20 different data formats
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“A biologist would rather share their toothbrush than their (gene) names”
Mike Ashburner
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YouTube loves to share
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100 million views per day
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114 apps
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<rdf:RDF xmlns="http://www.affymetrix.com/community/publications/affymetrix/tmsplice#"
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<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>
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RDF, OWL, SPARQL, GRDDL, WTF?
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The semantic web, not The Semantic Web
Lower case ‘s’, lower case ‘w’
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<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&DATA=CCDS9344">CCDS9344</a> </p></td></tr>
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<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&DATA=CCDS9344" rel="ccds">CCDS9344</a> </p></td></tr>
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Can our web site be our API?
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http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618
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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' );
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More data on our sites than through the API
(we’re not the only ones)
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RSS
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iCal
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XML
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RESTful service
Representational state
transfer
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psd-production/projects
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psd-production/projects
GET
RETRIEVE
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<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>
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psd-production/projects
POST
CREATE
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http://psd-production/projects/67
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http://psd-production/projects/67
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POST
UPDATE
http://psd-production/projects/67
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DELETE
DESTROY
http://psd-production/projects/67
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No installationNo setup
No fancy protocols
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All you need is curl
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Perl API
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Ruby API
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Tools
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ToolsWorkflows
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It’s all about the workflow
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Trace archive vs SSAHA
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Workflows are memes
Users add value
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YouTube knows memes
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Not invented here!
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Reproducibility
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Go with the flow
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Quickly define workflows
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Quickly reuse services
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Data
Explore
Service Service
Data
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Reuse workflows
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YouTube for workflows+
Yahoo! Pipes for biological data
=Never having to write another BLAST parser
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Design
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Stop hacking
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Program to interfaces
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“The interface is a contract between data provider and
data consumer” Lincoln Stein
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Design for reuse
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Code for maintenance
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Foster “accidental development”
114 YouTube apps
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However...
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Designing for reuse is hard
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With great power comesgreat responsibility
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With great power comesgreat responsibility
Available
Accessible
Reliable
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Discoverable:where is your web site?
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Design is for humans
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YouTube is ‘only’ an online video site
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A good UI outweighs smart features
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“Monolithic solutions always fail”
Graham Cameron
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Loose coupling rules
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Don’t reinvent Eclipse
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Thank you
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