bmg-pcl/scaffolds

WIP On-demand environments for learners who were unable to install software

Scaffolds

This repository contains links to online tools that will help learners follow lessons if they are having technical difficulties installing required software.

If you are administering a workshop, please visit our resource guide

Quick Links to resources

Lesson	JupyterHub	JupyterLab	RStudio (binder)	RStudio (cloud)
SWC Shell Novice
SWC Python Inflammation
SWC Python Gapminder
SWC R Inflammation				swc-r-novice-inflammation in RStudio Cloud
SWC R Gapminder				swc-r-novice-gapminder in RStudio Cloud
DC Ecology R				dc-ecology-r in RStudio Cloud
DC Ecology Python
DC Social Sciences R (Python version is not official)				dc-social-science in RStudio Cloud
DC Geospatial (R only)				dc-geospatial-r in RStudio Cloud
DC Genomics (non-R only)

Guide to Resources

These resources provide instances of python, R, and bash without the learner needing to install software.

Binder (https://mybinder.net)

This resource comes with everything pre-configured and will open in one of the JupyterHub, JupyterLab, or RStudio interfaces. There are limitations to this approach:

• startup can take anywhere from 30 seconds to 30 minutes, depending on when it was last built
• sessions expire with 10 minutes of inactivity
• data does not persist between sessions
• limited to 100 simultaneous users per session

The benefits for this is that there is no log in for users and it works directly in the browser.

RStudio Cloud (https://rstudio.cloud)

This resource is exclusively for R-based lessons. It requires a login from users, either through Google, GitHub, or on-site registration. The templates were created by hand and are not explicitly synched with this repository.

There are different tiers for this resource, the basic being the free tier, which most learners will be using and there are limitations:

• sessions expire after 10 minutes of activity
• users have 15 hours of computation time per month, which includes parallel computation and inactivity.

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How this repository works

This repository hosts this README file on the main (master) branch. All other branches on this repository are independent and contain the required data files and setup to run in either RStudio Cloud or My Binder.

Each new branch is created with the following command pair to first create the branch with no history and then remove all files.

git checkout --orphan <branchname>
git rm --cached -r .

The project can then be set up for the learner with the data set in a data/ directory and the setup instructions inside of a hidden .binder/ directory according to these set up rules: https://mybinder.readthedocs.io/en/latest/howto/index.html