Tutorial to introduce Plant CV data and software

[ghost]

Overview

(updated Feb 5 2017 by @dlebauer)

Write tutorial to introduce people to TERRA REF's plantCV dataset and pipeline

• PlantCV output in sample space https://terraref.ncsa.illinois.edu/clowder/datasets/589519294f0c0650d062913f?space=57e42cd44f0cff4b58dd3eea (this is in public sample space, you can add more).

This should go in the terraref/tutorials repository.

Completion Criteria

• [ ] a self-guided intro to the plantCV data and pipeline
  • intro may point to this video https://youtu.be/dCNYEl3ld0s of all steps from setting up pipeline to uploading / processing data
  • link to documentation of setting up Clowder
• [ ] explore a plantCV dataset in the Clowder interface (@rachelshekar)
  • Users should watch this video about how to start with Clowder web interface starting from 2m31s: https://youtu.be/dCNYEl3ld0s?t=2m31s
• [ ] @craig-willis perhaps write up instructions for using the the plantCV docker image terraref/computing-pipeline#244 from within ndslabs. Please download the sample dataset and put it in a folder path that replicates the one on Roger.
• [ ] demonstrate how to explore the sample dataset from within iPython and / or Rmd notebook (@nfahlgren)
  • cross reference extracting associated traits from BETYdb via url-API, e.g.
    • https://terraref.ncsa.illinois.edu/bety/api/beta/cultivars?name=&key=9999999999999999999999999999999999999999
    • see also / cross reference https://github.com/terraref/tutorials/blob/master/traits/02-danforth-phenotyping-facility.Rmd
• [ ] (further reading, i.e. links): how the plantCV pipeline can be adopted by other groups (@yanliu-chn)
  • video shows how to set up Clowder+PlantCV cloud system https://youtu.be/dCNYEl3ld0s
  • is there a tutorial or documentation for running the plantCV pipeline somewhere? Linking to this is sufficient

[nfahlgren]

Would this work? http://plantcv.readthedocs.io/en/latest/. We have multiple tutorials in our documentation. Or something more TERRA-REF specific?

[dlebauer]

It would be great to have something that uses terraref data for tutorials. On Tue, Jan 31, 2017 at 1:46 PM Noah Fahlgren notifications@github.com wrote:

Would this work? http://plantcv.readthedocs.io/en/latest/. We have multiple tutorials in our documentation. Or something more TERRA-REF specific?

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[dlebauer]

Issue moved to terraref/tutorials #2 via ZenHub