Rutger Vos19 December 2011
Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos        ...
Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos        ...
Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos        ...
Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos        ...
Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos        ...
Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos             1...
Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos             1...
Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos             1...
Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos             1...
Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos             1...
Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos             19 Decem...
Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos             19 Decem...
Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos             19 Decem...
Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos             19 Decem...
Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos             19 Decem...
Partners    NESCent    DBCLS    TDWG    iPlant    PRFRutger Vos                19 December 2011
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Vos at NCB Naturalis

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  • 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
  • Vos at NCB Naturalis

    1. 1. Rutger Vos19 December 2011
    2. 2. Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos 19 December 2011
    3. 3. Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos 19 December 2011
    4. 4. Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos 19 December 2011
    5. 5. Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos 19 December 2011
    6. 6. Research / Software / Outreach Phylogenetics Phylogenomics Cybertaxonomy Georeferencing InformaticsRutger Vos 19 December 2011
    7. 7. Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos 19 December 2011
    8. 8. Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos 19 December 2011
    9. 9. Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos 19 December 2011
    10. 10. Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos 19 December 2011
    11. 11. Research / Software / Outreach Toolkits Web sites and APIs Databases Unix pipelines StandardsRutger Vos 19 December 2011
    12. 12. Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos 19 December 2011
    13. 13. Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos 19 December 2011
    14. 14. Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos 19 December 2011
    15. 15. Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos 19 December 2011
    16. 16. Research / Software / Outreach Publishing Teaching Mentoring Communications HackathonsRutger Vos 19 December 2011
    17. 17. Partners  NESCent  DBCLS  TDWG  iPlant  PRFRutger Vos 19 December 2011
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