KEMBAR78
Talk about microBEnet (http://microbe.net) | PDF
The Microbiology of the
Built Environment Network
http://microBE.net
Jonathan A. Eisen
UC Davis
@phylogenomics
Saturday, May 25, 13
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, Summer
Williams
Saturday, May 25, 13
microBEnet Targets
• Those funded by Sloan Program
• Anyone in related fields w/ current or
potential interest in microBE
• Stakeholders
Saturday, May 25, 13
microBEnet Activities
1.Web site/hub
2.Organizing meetings and workshops
3.Creating and curating resources
4.Social media activities
5.Teaching how to share
Saturday, May 25, 13
microBEnet Activities
• Ideas wanted
Saturday, May 25, 13
Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13
Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13
Undergrad projects
Saturday, May 25, 13
Why Undergrad Projects
• Undergraduate research projects in the
built environment
• A form of outreach (blogging, etc)
• Develop teaching materials related to the
microbiology of the built environment
• Keep our lab in the loop
• A touch of useful data
Saturday, May 25, 13
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):
Saturday, May 25, 13
Undergrad Genome Project Blog
Saturday, May 25, 13
Aquarium Biogeography
• 6 students
• 16S surveys and
metagenomics in aquariums
• Looking at biogeography
and succession
• Using MBE tools
• Paper in progress
• Coordinated by Jenna Lang,
David Coil, Matt Haggerty
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
Saturday, May 25, 13
Saturday, May 25, 13
Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13
Citizen Microbiology
• Workshop at UC Davis
• ASM session (last week)
• Multiple projects
Saturday, May 25, 13
Project MERCCURI
• Sample International Space Station in
collaboration with Nanoracks
• Outreach by sampling at various public
events
• Collaboration with Science
Cheerleaders and Science for Citizens
• Darlene Cavalier, Summer Williams,
Mark Severance
• UCD: David Coil, Jenna Lang, Russell
Neches, et al.
Saturday, May 25, 13
Citizen Science
Saturday, May 25, 13
Crowdfunding/Crowdsourcing
Saturday, May 25, 13
Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13
Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13
Educate and Inform
Saturday, May 25, 13
Centralize Information
• Pull in blog posts and news from
other sources
• Updates to social media
• New papers
• Twitter hashtag (#microbenet)
Saturday, May 25, 13
Monthly Newsletter
• Summary of
blog posts
• “Resource of
the Month”
• “People Behind
the Science”
video series…
“Project of the
Month”
• Recent and
upcoming
meetings
Saturday, May 25, 13
Reference Collections
• 102 members
• 684 papers
• Curated Tags
Saturday, May 25, 13
Other Information-Related
• Curate and analyze reference
collections
• Simple guides
• Sloan Program
• Wikipedia curation
Saturday, May 25, 13
Sharing & Publicizing Sloan Work
Saturday, May 25, 13
Sharing & Publicizing Sloan Work
• Guest blog posts
• microBEnet posts
• Mendeley
• Video interviews
• Press
• Data sharing
• Pre and post publication
• Job postings
• Networking
Saturday, May 25, 13
Gaps
Saturday, May 25, 13
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 samples
Saturday, May 25, 13
Thanks
• Alfred P. Sloan Foundation
• microBEnet people: Hal Levin, David Coil, Mary Jo
Seminoff, Holly Bik, Jenna Lang, Russell Neches, Tom
Olson, 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, Dan
Smith, et al.
• Sloan Funded researchers / labs
• Others working in microBE topics
• Advice: Rob Dunn, Holly Menninger, Rob Knight,
manyothers
Saturday, May 25, 13

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

  • 1.
    The Microbiology ofthe Built Environment Network http://microBE.net Jonathan A. Eisen UC Davis @phylogenomics Saturday, May 25, 13
  • 2.
    microBEnet: Who? • UCDavis: • 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, Summer Williams Saturday, May 25, 13
  • 3.
    microBEnet Targets • Thosefunded by Sloan Program • Anyone in related fields w/ current or potential interest in microBE • Stakeholders Saturday, May 25, 13
  • 4.
    microBEnet Activities 1.Web site/hub 2.Organizingmeetings and workshops 3.Creating and curating resources 4.Social media activities 5.Teaching how to share Saturday, May 25, 13
  • 5.
    microBEnet Activities • Ideaswanted Saturday, May 25, 13
  • 6.
    Future (ideas from2012 Mtg) • Host resources that others have that could be helpful to share • Guest blog posts • Latest papers with background • More targeted workshops to develop interactions • Undergrad education • K-12 outreach • Public outreach Saturday, May 25, 13
  • 7.
    Future (ideas from2012 Mtg) • Host resources that others have that could be helpful to share • Guest blog posts • Latest papers with background • More targeted workshops to develop interactions • Undergrad education • K-12 outreach • Public outreach Saturday, May 25, 13
  • 8.
  • 9.
    Why Undergrad Projects •Undergraduate research projects in the built environment • A form of outreach (blogging, etc) • Develop teaching materials related to the microbiology of the built environment • Keep our lab in the loop • A touch of useful data Saturday, May 25, 13
  • 10.
    Reference Genomes • 7students • 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): Saturday, May 25, 13
  • 11.
    Undergrad Genome ProjectBlog Saturday, May 25, 13
  • 12.
    Aquarium Biogeography • 6students • 16S surveys and metagenomics in aquariums • Looking at biogeography and succession • Using MBE tools • Paper in progress • Coordinated by Jenna Lang, David Coil, Matt Haggerty 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 Saturday, May 25, 13
  • 13.
  • 14.
    Future (ideas from2012 Mtg) • Host resources that others have that could be helpful to share • Guest blog posts • Latest papers with background • More targeted workshops to develop interactions • Undergrad education • K-12 outreach • Public outreach Saturday, May 25, 13
  • 15.
    Citizen Microbiology • Workshopat UC Davis • ASM session (last week) • Multiple projects Saturday, May 25, 13
  • 16.
    Project MERCCURI • SampleInternational Space Station in collaboration with Nanoracks • Outreach by sampling at various public events • Collaboration with Science Cheerleaders and Science for Citizens • Darlene Cavalier, Summer Williams, Mark Severance • UCD: David Coil, Jenna Lang, Russell Neches, et al. Saturday, May 25, 13
  • 17.
  • 18.
  • 19.
    Future (ideas from2012 Mtg) • Host resources that others have that could be helpful to share • Guest blog posts • Latest papers with background • More targeted workshops to develop interactions • Undergrad education • K-12 outreach • Public outreach Saturday, May 25, 13
  • 20.
    Future (ideas from2012 Mtg) • Host resources that others have that could be helpful to share • Guest blog posts • Latest papers with background • More targeted workshops to develop interactions • Undergrad education • K-12 outreach • Public outreach Saturday, May 25, 13
  • 21.
  • 22.
    Centralize Information • Pullin blog posts and news from other sources • Updates to social media • New papers • Twitter hashtag (#microbenet) Saturday, May 25, 13
  • 23.
    Monthly Newsletter • Summaryof blog posts • “Resource of the Month” • “People Behind the Science” video series… “Project of the Month” • Recent and upcoming meetings Saturday, May 25, 13
  • 24.
    Reference Collections • 102members • 684 papers • Curated Tags Saturday, May 25, 13
  • 25.
    Other Information-Related • Curateand analyze reference collections • Simple guides • Sloan Program • Wikipedia curation Saturday, May 25, 13
  • 26.
    Sharing & PublicizingSloan Work Saturday, May 25, 13
  • 27.
    Sharing & PublicizingSloan Work • Guest blog posts • microBEnet posts • Mendeley • Video interviews • Press • Data sharing • Pre and post publication • Job postings • Networking Saturday, May 25, 13
  • 28.
  • 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 samples Saturday, May 25, 13
  • 30.
    Thanks • Alfred P.Sloan Foundation • microBEnet people: Hal Levin, David Coil, Mary Jo Seminoff, Holly Bik, Jenna Lang, Russell Neches, Tom Olson, 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, Dan Smith, et al. • Sloan Funded researchers / labs • Others working in microBE topics • Advice: Rob Dunn, Holly Menninger, Rob Knight, manyothers Saturday, May 25, 13