talk about microbenet ()
DESCRIPTION
Talk by Jonathan Eisen about microBEnet for 2013 meeting of the Sloan Foundation program on microbiology of the built environmentTRANSCRIPT
The Microbiology of the Built Environment Network
http://microBE.net
Jonathan A. EisenUC 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 workshops3.Creating and curating resources4.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 BharadwajHigh 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