2. Research / Software / Outreach
Phylogenetics
Phylogenomics
Cybertaxonomy
Georeferencing
Informatics
Rutger Vos 19 December 2011
3. Research / Software / Outreach
Phylogenetics
Phylogenomics
Cybertaxonomy
Georeferencing
Informatics
Rutger Vos 19 December 2011
4. Research / Software / Outreach
Phylogenetics
Phylogenomics
Cybertaxonomy
Georeferencing
Informatics
Rutger Vos 19 December 2011
5. Research / Software / Outreach
Phylogenetics
Phylogenomics
Cybertaxonomy
Georeferencing
Informatics
Rutger Vos 19 December 2011
6. Research / Software / Outreach
Phylogenetics
Phylogenomics
Cybertaxonomy
Georeferencing
Informatics
Rutger Vos 19 December 2011
7. Research / Software / Outreach
Toolkits
Web sites and APIs
Databases
Unix pipelines
Standards
Rutger Vos 19 December 2011
8. Research / Software / Outreach
Toolkits
Web sites and APIs
Databases
Unix pipelines
Standards
Rutger Vos 19 December 2011
9. Research / Software / Outreach
Toolkits
Web sites and APIs
Databases
Unix pipelines
Standards
Rutger Vos 19 December 2011
10. Research / Software / Outreach
Toolkits
Web sites and APIs
Databases
Unix pipelines
Standards
Rutger Vos 19 December 2011
11. Research / Software / Outreach
Toolkits
Web sites and APIs
Databases
Unix pipelines
Standards
Rutger Vos 19 December 2011
12. Research / Software / Outreach
Publishing
Teaching
Mentoring
Communications
Hackathons
Rutger Vos 19 December 2011
13. Research / Software / Outreach
Publishing
Teaching
Mentoring
Communications
Hackathons
Rutger Vos 19 December 2011
14. Research / Software / Outreach
Publishing
Teaching
Mentoring
Communications
Hackathons
Rutger Vos 19 December 2011
15. Research / Software / Outreach
Publishing
Teaching
Mentoring
Communications
Hackathons
Rutger Vos 19 December 2011
16. Research / Software / Outreach
Publishing
Teaching
Mentoring
Communications
Hackathons
Rutger Vos 19 December 2011
17. Partners
NESCent
DBCLS
TDWG
iPlant
PRF
Rutger Vos 19 December 2011
Notes de l'éditeur
Thank you for the invitation and for your timeWill take opportunity for blue sky talkNothing in X makes sense except in the light of YThe Tree of Life is thus central unifying concept of biologyMy long-term vision: the Tree of Life as central unifying artifact of biologyTree can be overgrown with (meta-)data, like the epiphytes on this tree
Large-scale phylogenetic inference: primates, mammals, AVATOLAssisted in phylogenetics in others’ research (alcids, stick insects, salmonids, mammal figure, apurva meta-analysis)
Lots of molecular data to relate to the tree of life (and back): function prediction, orthology assignment, studies of molecular evolutionExample: marie curie projectThis figure shows that loci that enrich GO terms for cell differentiation are especially expressed in the brains.Also worked on neanderthal short reads for dyslexia
Combining data from different sources usually means “joining” on species names/concepts/identifiersDealt with in a number of different contextsUsed NCBI taxon IDs, namebank identifiers, ToL node IDs, TreeBASE taxon IDs, “true” namesVery interested in doing similar joins with things such as scratchpads
Example figure shows geophylogeny for primates using GBIF occurrence dataHave added georeferencing to NeXML using DarwinCore termsHave implemented georeferencing (and export) in TreeBASEHave mentored phyloGeoRefGSoC student
Many interesting aspect to data per se:Publishing: licensing, attribution and provenance (ppod)Linking: linked data, identification, semantic webFigure shows LOD from two years ago, life sciences are in pink, Naturalis could be in there
Have worked on a number of toolkits/workflow environments:NeXML libraries for java/ruby/perlBio::Phylo/BioPerlMesquiteCIPRES/KeplerYahoo! PipesInterested in doing things with Taverna
Maintain a number of websites:Wikis for various projectsPRF public relationsNeXMLTreeBASEImplemented web services:TreeBASEuBio namebank/classification bankTimeTreeFile format translation and validationDeveloped PhyloWS web service specification
Lead developer for TreeBASE, obviously familiar with RDBMS/SQL. Also worked with NoSQL systems: couchdb, plucene, sesame
Learned UNIX in grad school for primate supertreeDeveloped and released marie curie pipelineWorked on beowulf (MPI) architectures at SFU/SDSC/UoRWould be comfortable working on HPC architectures here
Developed NeXML schemaCo-developed PhyloWS specContributing to CDAODeveloped TreeBASE ontologyHave idea for Visual language ontology
Several “highly accessed” articles (Bio::Phylo, BioHackathon), mammal supertree is very highly cited, NeXML coming out soon in SystBiol
Have taught ComPhy at NESCent, Gulbenkian, BGI, KyotoHave TA-ed lemur course in Amsterdam and Vancouver
Have mentored five GSoC students, maybe Naturalis could be hosting org for informatics students?
Public outreach person on the web for HIP and PRF: wikis, social media, websites. Important for standards evangelism, documentation of technologies. Would love to build NCB informatics portal.
What is a hackathon?(Co-)organized phyloinformatics hackathon, db interophackathon, biohackathon. Participated in TDWG VoCamp (Montpellier)
Organizations that help sustain various initiatives:TDWG: standards certification, evangelismiPlant: data integrationDBCLS/NESCent: hackathons, comphyPRF: TreeBASE, ToLWeb
