microBEnet talk for #AAASMobe by @phylogenomics - March 27, 2014

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Talk by Jonathan Eisen about the "microbiology of the built environment network" for the meeting "Microbiomes of the Built Environment" in Washington, DC on March 27, 2014.

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microBEnet talk for #AAASMobe by @phylogenomics - March 27, 2014

  1. 1. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? microBEnet: microbiology of the Built Environment network ! Jonathan A. Eisen University of California, Davis ! March 27, 2014 #AAASMoBe meeting
  2. 2. 2010 • The Alfred P. Sloan Foundation announced calls for proposals for a new “Indoor Environment Program” • One project would be to 
 
 “… establish an interdisciplinary network of researchers and practitioners that will build the community, operate community web resources, and organize specialized workshops …”
  3. 3. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/
  4. 4. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
  5. 5. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  6. 6. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  7. 7. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  8. 8. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing microBEnet Goals • Knowledge dissemination • Networking • Catalyzing collaboration • Gap filling • Producing resources • Teaching openness
  9. 9. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing microBEnet Goals • 2011 Session at Indoor Air • 2011 Citizen Microbiology • 2012 Session at Lake Arrowhead Small Genomes • 2012 Session at Healthy Buildings • 2012 VAMPS/QIIME • 2013 Citizen Microbiology at ASM • 2013 QIIME Workshops • 2013 GSC13 • 2014 Publish or Perish
  10. 10. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Education Openness & Sharing microBEnet Future Plans/Ideas • Animals in the BE • Closed ecosystems • Eukaryotes in the BE • Culture collections and reference genomes • Building Science Education • Antimicrobials in the BE • Software Carpentry • Bioinformatics workshops • Ideas wanted
  11. 11. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  12. 12. http:// www.google. com/ Digital and Social Science New Paper Blog Post Twitter Facebook Page LinkedIn GroupPubmed Commons Mendeley
  13. 13. http:// www.google. com/ Digital and Social Science New Paper Twitter Facebook Page LinkedIn GroupMendeley
  14. 14. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
  15. 15. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
  16. 16. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
  17. 17. http:// www.google. com/ Digital and Social Science Meeting Storify Twitter Facebook Page LinkedIn GroupBlog
  18. 18. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
  19. 19. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  20. 20. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://en.wikipedia.org/wiki/File:TsunamiHazardSign.svg
  21. 21. http:// www.google. com/ Digital and Social Science New Paper Blog Post Twitter Facebook Page LinkedIn GroupPubmed Commons Mendeley
  22. 22. http:// www.google. com/ Social Reference Collections • 140 members • >877 papers • Curated Tags
  23. 23. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Author Contacts Google Scholar Pages Tagging Blog Journal Club New People’s Starting Point RSS Feeds
  24. 24. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Newman M E J PNAS 2004;101:5200-5205 Gaps in the Field Full Text DB Co-authorship Networks
  25. 25. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  26. 26. http:// www.google. com/ Collaborative Micro Edu/research
  27. 27. http:// www.google. com/ BE Reference Genomes • 7 students • Cultured organisms isolated from a variety of built environments • Identify, sequence, assemble, annotate, publish a genome each • 5 papers published so far in Genome Announcements • All Data released • Student blog • Brachybacterium muris (Jonathon Lo): • Microbacterium sp (Zach Bendiks): • Curtobacterium flaccumfaciens (Jennifer Flanagan) • Dietzia sp (Amanda Diep): • Kocuria rosea (Jessica Doctor): • Leucobacter sp (Dakota Bevans, Hannah Holland-Moritz):
  28. 28. http:// www.google. com/ Swab to Genome Workflow Dunitz et al. in prep
  29. 29. http:// www.google. com/ Aquarium Biogeography • Biogeography and succession • Extensive chemical “metadata” collected • 16S surveys and metagenomics • Using MBE tools • Coordinated by Jenna Lang, David Coil, Matt Haggerty • Advice from Josh Neufeld & Laura Sauder • Papers in progress Undergraduates: •Sabreen Aulakh •Alex Alexiev •Akshay Sethi •Andrew Shaver •Jennifer Flanagan •Lakshmi Bharadwaj High School: •Kevin Yang •In collaboration with Kenneth Kubo at American River College !
  30. 30. http:// www.google. com/ Citizen Microbiology
  31. 31. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  32. 32. http:// www.google. com/ The Rise of Citizen Science
  33. 33. http:// www.google. com/ Citizen Microbiology Meetings
  34. 34. http:// www.google. com/ Home Microbiome Slide from Jack Gilbert, PI on Project
  35. 35. http:// www.google. com/ Wild Life of Your Home Slide from Holly Menninger, CoPI on the project
  36. 36. http:// www.google. com/ Project MERRCURI
  37. 37. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  38. 38. http:// www.google. com/ Teaching and Spreading Openness • Open Access publishing • Repositories and preprints • Open Data release • Data and Metadata publishing • Open Source Software • CC licenses on digital products • Recording and posting talks, slides • Post publication peer review
  39. 39. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  40. 40. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing What Next? Sustainability More BE/BS Press Forward Wikipedia Integration RewardsMatchmaking Network Analysis Protocols Training on use Reporter Guides
  41. 41. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/

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