MoBeDACMicrobiome of the Built Environment Data Analysis Core
Background Rob Knight’s group, University of Colorado at Boulder Since we’re talking about air quality…
Boulder, Colorado
Boulder, Colorado
Boulder, Colorado
Right now…
Right now…
Right now…
About the Knight Lab Rob Knight, PhD, PI, Smartypants Qiime – Quantitative Insights Into Microbial Ecology Qiime on the...
Why do we need standards? Everyone likes the idea Everyone uses their own standard Problem: Leads to situations such as...
It’s a cat.
Or maybe a shark?
Such a nice monkey…
Err wait, is it a walrus?
A local…
Or… a dolphin?
Unexpected Results Different tools can (and do!) lead to different results Answer: speak the same language
Presenting MoBeDAC   Central repository for microbial metadata and sequence data   Implements and enforces metadata stan...
MoBeDAC Overview
Metadata: GSC Checklists
Metadata: GSC Checklists
The Technology Platform Agnostic – keep it really simple REST API for communication JSON for encoding
REST – Representational State Transfer Sounds really fancy… but it’s really simple:     Usually runs over HTTP     Not ...
JSON – JavaScript Object Notation   Sounds fancy too… but it’s:       Ubiquitous       Simple, human readable       If...
Resources   MoBeDAC                                           Microbe.net       http://mobedac.org                     ...
Thanks! Questions?
MoBeDAC - Microbiome of the Built Environment Data Analysis Core
MoBeDAC - Microbiome of the Built Environment Data Analysis Core
MoBeDAC - Microbiome of the Built Environment Data Analysis Core
MoBeDAC - Microbiome of the Built Environment Data Analysis Core
MoBeDAC - Microbiome of the Built Environment Data Analysis Core
MoBeDAC - Microbiome of the Built Environment Data Analysis Core
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MoBeDAC - Microbiome of the Built Environment Data Analysis Core

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MoBeDAC - Microbiome of the Built Environment Data Analysis Core. This slideshow was presented at the Healthy Buildings 2012 conference in Brisbane Australia. Material covers the MoBeDAC and how it integrates various data sources and enables analysis across platforms.

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MoBeDAC - Microbiome of the Built Environment Data Analysis Core

  1. MoBeDACMicrobiome of the Built Environment Data Analysis Core
  2. Background Rob Knight’s group, University of Colorado at Boulder Since we’re talking about air quality…
  3. Boulder, Colorado
  4. Boulder, Colorado
  5. Boulder, Colorado
  6. Right now…
  7. Right now…
  8. Right now…
  9. About the Knight Lab Rob Knight, PhD, PI, Smartypants Qiime – Quantitative Insights Into Microbial Ecology Qiime on the web, data transport, MoBeDAC, etc… Spend a lot of time on standards and data consistency
  10. Why do we need standards? Everyone likes the idea Everyone uses their own standard Problem: Leads to situations such as this…
  11. It’s a cat.
  12. Or maybe a shark?
  13. Such a nice monkey…
  14. Err wait, is it a walrus?
  15. A local…
  16. Or… a dolphin?
  17. Unexpected Results Different tools can (and do!) lead to different results Answer: speak the same language
  18. Presenting MoBeDAC Central repository for microbial metadata and sequence data Implements and enforces metadata standards – GSC checklists Enforces sequence data consistency – quality filtering, trimming Brings together an array of utilities and resources:  VAMPS  MG-RAST  Qiime  FungiDB  Microbe.net  Future platforms via open API
  19. MoBeDAC Overview
  20. Metadata: GSC Checklists
  21. Metadata: GSC Checklists
  22. The Technology Platform Agnostic – keep it really simple REST API for communication JSON for encoding
  23. REST – Representational State Transfer Sounds really fancy… but it’s really simple:  Usually runs over HTTP  Not a standard per-se, a series of guidelines. Flexible. Only 4 Commands (verbs):  GET - List resources or elements of resource  PUT - Replace entire collection with new data  POST - Add new item to collection  DELETE - Remove item or collection WWW is the largest REST system – everyone uses it without knowing
  24. JSON – JavaScript Object Notation Sounds fancy too… but it’s:  Ubiquitous  Simple, human readable  If you have data, put lots of brackets around it  Send it For example:  If I have a dictionary that looks like: a: apple b: bunny c: kitty shark JSON says it should look like: {"a": "apple", "c": "kitty shark", "b": "bunny"} Current MoBeDAC API specification available at: http://metagenomics.anl.gov/Html/api.html
  25. Resources MoBeDAC  Microbe.net  http://mobedac.org  http://www.microbe.net/ VAMPS  GSC  http://vamps.mbl.edu  http://gensc.org MG-RAST  BE Package Terms  http://metagenomics.anl.gov  http://www.microbe.net/wp- content/uploads/2012/05/built_environm Qiime ent-metadata-terms-v51.xls  http://microbio.me/qiime http://www.qiime.org/  Sloan Foundation  http://www.sloan.org/ FungiDB  http://fungidb.org/fungidb.b2
  26. Thanks! Questions?

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