microBEnet talk for #AAASMobe by @phylogenomics - March 27, 2014
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Transcript of microBEnet talk for #AAASMobe by @phylogenomics - March 27, 2014
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microBEnet: microbiology of the Built Environment network
!Jonathan A. Eisen
University of California, Davis !
March 27, 2014 #AAASMoBe meeting
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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Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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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
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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
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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
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Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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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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om/url?
Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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com/
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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 &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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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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Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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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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Meetings &
Workshops
Citizen Science
Digital &
Social Media
Information (Overload)
Education
Openness &
Sharing
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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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Meetings &
Workshops
Citizen Science
Digital &
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Information (Overload)
Education
Openness &
Sharing
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Meetings &
WorkshopsCitizen 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
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