Talk about microBEnet ()

The Microbiology of the Built Environment Network

http://microBE.net

Jonathan A. EisenUC Davis

@phylogenomics

Saturday, May 25, 13

http://microBE.net

http://microBE.net

http://microBE.net

http://microBE.net

http://microBE.net

http://microBE.net

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


microBEnet Targets

• Those funded by Sloan Program• Anyone in related fields w/ current or

potential interest in microBE• Stakeholders


microBEnet Activities

1.Web site/hub 2.Organizing meetings and workshops3.Creating and curating resources4.Social media activities 5.Teaching how to share


microBEnet Activities

• Ideas wanted


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


Undergrad projects


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


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):


Undergrad Genome Project Blog


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


Citizen Microbiology

• Workshop at UC Davis• ASM session (last week)• Multiple projects


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.


Citizen Science


Crowdfunding/Crowdsourcing


Educate and Inform


Centralize Information

• Pull in blog posts and news from other sources

• Updates to social media• New papers• Twitter hashtag (#microbenet)


Monthly Newsletter

• Summary of blog posts

• “Resource of the Month”

• “People Behind the Science” video series… “Project of the Month”

• Recent and upcoming meetings


Reference Collections

• 102 members• 684 papers• Curated Tags


Other Information-Related

• Curate and analyze reference collections

• Simple guides• Sloan Program• Wikipedia curation


Sharing & Publicizing Sloan Work


Sharing & Publicizing Sloan Work

• Guest blog posts• microBEnet posts• Mendeley• Video interviews• Press• Data sharing• Pre and post publication• Job postings• Networking


Gaps


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


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


Talk about microBEnet ()

Health & Medicine

Transcript of Talk about microBEnet ()