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 &

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Citizen Science

Digital &

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Information (Overload)

Education

Openness &

Sharing

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Meetings &

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Citizen Science

Digital &

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Information (Overload)

Education

Openness &

Sharing

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Meetings &

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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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Citizen Science

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Education

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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 &

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Citizen Science

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Education

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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 &

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Citizen Science

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Education

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Digital and Social Science

New Paper

Blog Post

Twitter

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

Twitter

Facebook Page

LinkedIn GroupBlog

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Meetings &

Workshops

Citizen Science

Digital &

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Information (Overload)

Education

Openness &

Sharing

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Digital and Social Science

New Paper

Blog Post

Twitter

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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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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Meetings &

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Citizen Science

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Education

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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 &

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Citizen Science

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Education

Openness &

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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 &

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Citizen Science

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Education

Openness &

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Meetings &

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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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