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Vos at NCB Naturalis
- 1. Rutger Vos 19 December 2011
- 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
Notas do Editor
- 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