neon-science-summit-2019

Example Notebooks for NEON Science Summit Planet Labs breakout session

Cloning a GitHub Repository

Clone this repository - there are example .ipynb notebooks for you to work with.

git clone https://github.com/cyverse-gis/neon-science-summit-2019

Find and download NEON data with our R Shiny App

Run the Shiny app in RStudio

Clone the Shiny App repository

git clone https://github.com/cyverse-gis/neon-shiny-browser

Change your RStudio working directory to the location of the app:

getwd()
setwd("~/neon-shiny-browser")

Load Shiny and run the app (note - the app has numerous spatial dependencies which must also be installed if running on a local machine, this can take some time).

library(shiny)
runApp()

Run Shiny app in CyVerse

Select the NEON-Shiny-Browser App in CyVerse.

Browse and download data to the Data Store.

View downloaded data in your home folder /analyses

Run Shiny app with Docker locally or on a Virtual Machine

Download from DockerHub:

docker pull cyversevice/shiny-geospatial:neon-shiny-browser

Or just run the app:

docker run -it --rm -p 3838:3838 -e REDIRECT_URL=http://localhost:3838 -v ~/NEON_Downloads:/NEON_Downloads cyversevice/shiny-geospatial:neon-shiny-browser

Download Planet Labs data with Jupyter Lab

Launch with

Citation:

Samapriya Roy. (2019, October 14). samapriya/neon-science-summit-2019: neon-science-summit-2019 (Version 0.1). Zenodo.
http://doi.org/10.5281/zenodo.3484160

Run Jupyter Lab on your own computer

You will need to install numerous dependencies for running the Lab

Run Jupyter Lab with Docker

docker run -it --rm -v /$HOME:/app --workdir /app -p 8888:8888 -e REDIRECT_URL=http://localhost:8888 cyversevice/jupyterlab-scipy:planet-latest

Note you may need to mount the location of your NEON Data when you start the container

-v ~/NEON_Downloads:/NEON_Downloads

Run Jupyter Lab using CyVerse VICE

CyVerse hosts a data science workbench called the Discovery Environment. You can launch visual and interactive compute environments (VICE) containers from the DE.

Steps:

(1) Register for CyVerse https://user.cyverse.org/

(2) Log into the Discovery Environment: https://de.cyverse.org

(3) Open the Apps tab and search for "Jupyter Lab Planet" and find the corresponding public app, or use this Quick Launch