fhdsl / gdscn_biodigs_soil

This is a BioDIGS in the Classroom companion guide for the BioDIGS project. This particular activity guides students through exploration and visualization of the soil characteristics data using R.

BioDIGS in the Classroom: Exploring Soil Data

This course was created from the AnVIL Template, which is based on the OTTR Template

You can see the rendered course material here

About this course

This activity guides students through exploration of the BioDIGS soil data using the tidyverse in R. Students will learn basic data summarization and visualization skills. It is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website here for more information about this collaborative, distributed research project, including how you can get involved!

The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives here.

Target Audience

The activities in this guide are written for undergraduate students and beginning graduate students. Some sections require basic understanding of the R programming language, which is indicated at the beginning of the chapter.

Platform

The activities in this guide are demonstrated on NHGRI's AnVIL cloud computing platform. AnVIL is the preferred computing platform for the GDSCN. However, all of these activities can be done using your personal installation of R or using the online Galaxy portal.

Data

The data generated by the BioDIGS project is available as an R package (BioDIGSData, https://github.com/fhdsl/BioDIGSData), through the BioDIGS website, or through an AnVIL workspace.

Data about the soil itself as well as soil metal content was generated by the Delaware Soil Testing Program at the University of Delaware. Sequences were generated by the Johns Hopkins University Genetic Resources Core Facility and by PacBio.

Encountering problems?

If you are encountering any problems with this course, please file a GitHub issue or contact Ava Hoffman (ahoffma2 at fredhutch.org) or Elizabeth Humphries (ehumphri at fredhutch.org).

All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise.

gdscn_biodigs_soil's Issues

New Course - Set Repository Settings

For more information on these settings see instructions in the getting started GitHub wiki pages.

• This course repository is set to public.

• Add the jhudsl-robot as a collaborator to your repository..

• GH_PAT has been set up as a GitHub secret

• GitHub pages is turned on

  • Go to Settings > Pages. Underneath Source, choose main for the branch and select the docs folder. Then click Save.
  • Check Enforce HTTPS.

• Github secret GH_PAT has been set
  Name: GH_PAT
value: A personal access token following these instructions.
  Underneath Select scopes, check both repo and workflow.
  Then copy the PAT and save as the value.

• Set branch protections settings

  • main branch has been set up:
    • Require pull request reviews before merging box is checked.
    • Require status checks to pass before merging box is checked.
      • Underneath that Require branches to be up to date before merging box is checked.
  • Click Save at the bottom of the page!

• Customize GitHub actions for what you will need in this course.

Restore build badge

Similar to what was done here: fhdsl/GDSCN_BioDIGS_Book#34

New Course - Templates to Edit

Follow the Wiki instructions here for details on how to complete the items in this issue.

The following files need to be edited to get this new course started!

Files that need edited upon creating a new course.

• README.md - Fill in all the { }.
• index.Rmd - title: should be updated.
• 01-intro.Rmd - replace the information there with information pertinent to this new course.
• 02-chapter_of_course.Rmd - This Rmd has examples of how to set things up, if you don't need it as a reference, it can be deleted.

Files that need to be edited upon adding each new chapter (including upon creating a new course):

• _bookdown.yml - The list of Rmd files that need to be rendered needs to be updated. See instructions.
• book.bib - any citations need to be added. See instructions.

Picking a style

See more about customizing style on this page in the guide.
By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.

Using a style set

Read more about the style sets here.

• On a new branch, copy the style-sets/<set-name>/index.Rmd and style-sets/<set-name>/_output.yml to the top of the repository to overwrite the default index.Rmd and _output.yml.
• Copy over all the files in the style-sets/<set-name>/copy-to-assets to the assets folder in the top of the repository.
• Create a pull request with these changes, and double check the rendered preview to make sure that the style is what you are looking for.

Files that need to be edited upon adding new packages that the book's code uses:

• docker/Dockerfile needs to have the new package added so it will be installed. See instructions.
• The code chunk in index.Rmd should be edited to add the new package.

Reminder - Add user feedback method

To help users report issues or areas of improvement for your course, you should provide a clear method of feedback for your users to route their concerns through.

A feedback method (Google Form) has already been provided for AnVIL and GDSCN courses. Github actions automatically populates the Google Form with the title field from index.Rmd using the AnVIL Feedback Script.

• The title field has been filled out in the header yaml of index.Rmd.

No further action is needed on your part. However, if you would like to change the feedback method, you can do so by editing this line of code in _output.yml.

See these instructions for how to manually create a feedback link for AnVIL / GDSCN content or events.

New Course - Template Update Enrollment

The original template: https://github.com/jhudsl/OTTR_Template is always a work in progress.
We are working on adding more features and smoothing out bugs as we go. The AnVIL Template collects these and can pass them along to this repository.

If you want to receive updates from the AnVIL template to your course template, you will need to enroll this repository to the template updates by adding it to the sync.yml file.

• Follow these instructions to enroll your course repository to receive these updates.

• Ensure that you have followed these instructions to add the jhudsl-robot as a collaborator to your repository.

New Course - Add Repo to AnVIL Collection

If you want this repository to be added to the AnVIL Collection, make sure you do the following:

• Click the gear icon on the top right of the "Code" page next to "About"
• Create a repository description
• Add the homepage where your course will be rendered
• Add a description of your course/content
• Add the topic tag anvil or gdscn. You should also supply any other relevant tags.

Following these steps will also automatically add this repository to the AnVIL Collection if this repository is owned by one of the DaSL organizations.

For more information on these settings see instructions in the wiki pages.

For more information about adding repositories to the DaSL Collection, see the AnVIL Collection README.