microbenet talk for #aaasmobe by @phylogenomics - march 27, 2014
DESCRIPTION
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.TRANSCRIPT
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microBEnet: microbiology of the Built Environment network
!Jonathan A. Eisen
University of California, Davis !
March 27, 2014 #AAASMoBe meeting
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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 …”
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microBEnet
Goals • Knowledge dissemination • Networking • Catalyzing collaboration • Gap filling • Producing resources • Teaching openness
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Meetings &
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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
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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
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Digital and Social Science
New Paper
Blog Post
Facebook Page
LinkedIn GroupPubmed
CommonsMendeley
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Digital and Social Science
New Paper Twitter
Facebook Page
LinkedIn GroupMendeley
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Digital and Social Science
Meeting
Storify
Facebook Page
LinkedIn GroupBlog
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Digital and Social Science
New Paper
Blog Post
Facebook Page
LinkedIn GroupPubmed
CommonsMendeley
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Social Reference Collections
• 140 members • >877 papers • Curated Tags
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Author Contacts
Google Scholar PagesTagging
Blog Journal Club
New People’s Starting Point
RSS Feeds
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Newman M E J PNAS 2004;101:5200-5205
Gaps in the FieldFull Text DB
Co-authorship Networks
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Meetings &
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Information (Overload)
Education
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Collaborative Micro Edu/research
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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):
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Swab to Genome Workflow
Dunitz et al. in prep
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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 !
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Citizen Microbiology
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The Rise of Citizen Science
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Citizen Microbiology Meetings
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Home Microbiome
Slide from Jack Gilbert, PI on Project
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Wild Life of Your Home
Slide from Holly Menninger, CoPI on the project
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Project MERRCURI
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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
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What Next?
Sustainability
More BE/BS
Press Forward
Wikipedia Integration
RewardsMatchmaking
Network Analysis
Protocols
Training on use
Reporter Guides
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