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Talk about microBEnet (http://microbe.net)

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Talk by Jonathan Eisen about microBEnet for 2013 meeting of the Sloan Foundation program on microbiology of the built environment

Talk by Jonathan Eisen about microBEnet for 2013 meeting of the Sloan Foundation program on microbiology of the built environment


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  • 1. The Microbiology of theBuilt Environment Networkhttp://microBE.netJonathan A. EisenUC Davis@phylogenomicsSaturday, May 25, 13
  • 2. microBEnet: Who?• UC Davis:• Jonathan Eisen• David Coil• Mary Jo Seminoff• Holly Bik• Tom Olson• Russell Neches• Jenna Lang• many undergrads• Building Ecology Research Group:• Hal Levin• Other collaborators• Jessica Green• Jack Gilbert, Dan Smith, others at Argonne and U. Chicago• Darlene Cavalier, Wendy Brown, Mark Severance, SummerWilliamsSaturday, May 25, 13
  • 3. microBEnet Targets• Those funded by Sloan Program• Anyone in related fields w/ current orpotential interest in microBE• StakeholdersSaturday, May 25, 13
  • 4. microBEnet Activities1.Web site/hub2.Organizing meetings and workshops3.Creating and curating resources4.Social media activities5.Teaching how to shareSaturday, May 25, 13
  • 5. microBEnet Activities• Ideas wantedSaturday, May 25, 13
  • 6. Future (ideas from 2012 Mtg)• Host resources that others have thatcould be helpful to share• Guest blog posts• Latest papers with background• More targeted workshops to developinteractions• Undergrad education• K-12 outreach• Public outreachSaturday, May 25, 13
  • 7. Future (ideas from 2012 Mtg)• Host resources that others have thatcould be helpful to share• Guest blog posts• Latest papers with background• More targeted workshops to developinteractions• Undergrad education• K-12 outreach• Public outreachSaturday, May 25, 13
  • 8. Undergrad projectsSaturday, May 25, 13
  • 9. Why Undergrad Projects• Undergraduate research projects in thebuilt environment• A form of outreach (blogging, etc)• Develop teaching materials related to themicrobiology of the built environment• Keep our lab in the loop• A touch of useful dataSaturday, May 25, 13
  • 10. Reference Genomes• 7 students• Cultured organismsisolated from a variety ofbuilt environments• Identify, sequence,assemble, annotate,publish a genome each• 5 papers published so far inGenome Announcements• All Data released• Student blog•Brachybacterium muris(Jonathon Lo):•Microbacterium sp (ZachBendiks):•Curtobacterium flaccumfaciens(Jennifer Flanagan)•Dietzia sp (Amanda Diep):•Kocuria rosea (Jessica Doctor):•Leucobacter sp (Dakota Bevans,Hannah Holland-Moritz):Saturday, May 25, 13
  • 11. Undergrad Genome Project BlogSaturday, May 25, 13
  • 12. Aquarium Biogeography• 6 students• 16S surveys andmetagenomics in aquariums• Looking at biogeographyand succession• Using MBE tools• Paper in progress• Coordinated by Jenna Lang,David Coil, Matt HaggertyUndergraduates:•Sabreen Aulakh•Alex Alexiev•Akshay Sethi•Andrew Shaver•Jennifer Flanagan•Lakshmi BharadwajHigh School:•Kevin Yang•In collaboration with KennethKubo at American RiverCollegeSaturday, May 25, 13
  • 13. Saturday, May 25, 13
  • 14. Future (ideas from 2012 Mtg)• Host resources that others have thatcould be helpful to share• Guest blog posts• Latest papers with background• More targeted workshops to developinteractions• Undergrad education• K-12 outreach• Public outreachSaturday, May 25, 13
  • 15. Citizen Microbiology• Workshop at UC Davis• ASM session (last week)• Multiple projectsSaturday, May 25, 13
  • 16. Project MERCCURI• Sample International Space Station incollaboration with Nanoracks• Outreach by sampling at various publicevents• Collaboration with ScienceCheerleaders and Science for Citizens• Darlene Cavalier, Summer Williams,Mark Severance• UCD: David Coil, Jenna Lang, RussellNeches, et al.Saturday, May 25, 13
  • 17. Citizen ScienceSaturday, May 25, 13
  • 18. Crowdfunding/CrowdsourcingSaturday, May 25, 13
  • 19. Future (ideas from 2012 Mtg)• Host resources that others have thatcould be helpful to share• Guest blog posts• Latest papers with background• More targeted workshops to developinteractions• Undergrad education• K-12 outreach• Public outreachSaturday, May 25, 13
  • 20. Future (ideas from 2012 Mtg)• Host resources that others have thatcould be helpful to share• Guest blog posts• Latest papers with background• More targeted workshops to developinteractions• Undergrad education• K-12 outreach• Public outreachSaturday, May 25, 13
  • 21. Educate and InformSaturday, May 25, 13
  • 22. Centralize Information• Pull in blog posts and news fromother sources• Updates to social media• New papers• Twitter hashtag (#microbenet)Saturday, May 25, 13
  • 23. Monthly Newsletter• Summary ofblog posts• “Resource ofthe Month”• “People Behindthe Science”video series…“Project of theMonth”• Recent andupcomingmeetingsSaturday, May 25, 13
  • 24. Reference Collections• 102 members• 684 papers• Curated TagsSaturday, May 25, 13
  • 25. Other Information-Related• Curate and analyze referencecollections• Simple guides• Sloan Program• Wikipedia curationSaturday, May 25, 13
  • 26. Sharing & Publicizing Sloan WorkSaturday, May 25, 13
  • 27. Sharing & Publicizing Sloan Work• Guest blog posts• microBEnet posts• Mendeley• Video interviews• Press• Data sharing• Pre and post publication• Job postings• NetworkingSaturday, May 25, 13
  • 28. GapsSaturday, May 25, 13
  • 29. Gaps• Citizen microbiology• QIIME/VAMPS use• Software Carpentry• Culture collections• Genomes of isolates• How to share• Methods sharing• Other related social media• Alt metrics• Simulated community samplesSaturday, May 25, 13
  • 30. Thanks• Alfred P. Sloan Foundation• microBEnet people: Hal Levin, David Coil, Mary JoSeminoff, Holly Bik, Jenna Lang, Russell Neches, TomOlson, et al• All the undergrads in the lab• Science Cheerleaders and Science for Citizens esp.Darlene Cavalier, Wendy Brown, Mark Severance,Summer Williams• Collaborators: Jessica Green, Jack Gilbert, DanSmith, et al.• Sloan Funded researchers / labs• Others working in microBE topics• Advice: Rob Dunn, Holly Menninger, Rob Knight,manyothersSaturday, May 25, 13