Vos at NCB Naturalis
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The document outlines the research areas and activities of Rutger Vos, including phylogenetics, phylogenomics, cybertaxonomy, georeferencing, informatics, toolkits, websites, databases, teaching, mentoring, publishing, and partnerships with various organizations. It is dated December 19, 2011.
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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
Editor's Notes
- 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