BioWeatherMap At Active Research


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I gave a lightning talk at at RailsConf 2009 about

The BioWeatherMap initiative is a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life. Utilizing the power of high-throughput, low cost DNA sequencing and harnessing the drive of an enlightened public we propose a new collaborative research approach aimed at generating a steady stream of environmental samples from many geographic locations to produce high quality data for ongoing discovery and surveillance. Our approach will provide a unique opportunity to engage the public in the scientific research process while we address fundamental questions such as “How diverse is the microbial life around us?” and “How do microbial communities in different habitats change over time?” and “How can advanced sequencing technologies best be utilized to address issues in biodiversity, public health, and biosurveillance?”

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  • These questions are about the things around us.
    This is my friend, Jason Bobe. He works for the Personal Genome Project with George Church.

  • New sequencing technologies let us
    characterize the diversity of microbial life directly from the environment,
    increasing our ability to answer basic questions like “What lives around us?”.
  • There are a bunch of sufaces that you touch on a daily basis
    What do the microbiomes on those surfaces look like,
    and how do they change seasonally? annually?
  • Can citizens’ participation help track epidemics?
    How does the microbial diversity of soil impacts crop yields?
    How does the composition of microbes in outdoor air change with environmental conditions?
  • Sequencing is cheap, and getting cheaper - ~$60K for 1Mbase 454 read
    The BioWeatherMap project is an experiment in citizen science, in collaborative environmental discovery.

  • Enter as an individual or team. Staff will work with volunteers to identify appropriate surfaces, e.g. cross-walk buttons.

  • Attend the BioWeatherMap event in your city.
    Registered teams will be provided specimen collection supplies.  Tentative dates for BioWeatherMap events are weekends in May, June, and/or July. 

  • Collect: Collect residue/specimen from an approved public surface.  Record the date, time, weather, geolocation, and other data relevant to the specimen collected. 

  • Ship: The event organizer will collect all swabs the day of the event and ship them to a sequencing facility.

  • Sequence: The microbial DNA on the sterile swab will be characterized via 16S ribosomal RNA gene sequencing, uniquely identifying the bacteria present in the specimen.  We'll be using the 454 FLX/Titanium sequencing platform.

  • Publish: The sequence data will be made publicly available via an open access repository (CC0 universal waiver of rights). 

  • Visualize: Tools for processing the data will be implemented in a public computing environment, e.g. Google AppEngine. The community will analyze the data and create visualizations, e.g. similar to 

  • There are three main areas of core infrastructure that need to be rolled out to support the first run.

  • Swabbed crosswalks in the Boston area, confirmed that we can plate and grow samples -> there is life to sequence!

    Applying for funding from variety of sources.

  • BioWeatherMap At Active Research

    1. 1. ActiveResearch 2009 Jason Morrison
    2. 2. Questions
    3. 3. How diverse is the microbial life around us?
    4. 4. How do microbial communities in different habitats change over time?
    5. 5. How can advanced sequencing technologies be applied to biodiversity, public health, and biosurveillance?
    6. 6. Let’s find out!
    7. 7. Step 1 of 7 Register
    8. 8. Step 2 of 7 Converge
    9. 9. Step 3 of 7 Collect
    10. 10. Step 4 of 7 Ship
    11. 11. Step 5 of 7 Sequence
    12. 12. Step 6 of 7 Publish
    13. 13. Step 7 of 7 Visualize
    14. 14. Code
    15. 15. Event organization
    16. 16. Data collection, publication, and annotation
    17. 17. Visualization showcase broad .mit.e du org se. efu .pr are fl
    18. 18. Conclusion
    19. 19. Current Progress
    20. 20. Summer 2009 Pilot 300-500 samples Boston * San Francisco New York City * Seattle Washington D.C. * Kenya
    21. 21. Jason Morrison, ActiveResearch 2009 Thank you!
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