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Websites & Documentation

This website is rendered using a ReadTheDocs.org template. Think of RTD as “Continuous Documentation”.

ReadTheDocs has become a popular tool for developing web-based documentation. CyVerse Learning Materials Github hosts a few templates which you can view and pull for your own use.

Bookdown is an open-source R package that facilitates writing books and long-form articles/reports with R Markdown.

GitHub Pages using Jekyll, are another popular way of hosting websites on GitHub.

Confluence Wikis (CyVerse) are another tool for documenting your workflow.

Some things to remember

ReadTheDocs

  • publishing websites via ReadTheDocs.com costs money.
  • You can work in an offline state, where you develop the materials and publish them to your localhost using Sphinx
  • You can work on a website template in a GitHub repository, and pushes are updated in near real time using ReadTheDocs.com.

Bookdown

GitHub Pages

  • You can pull templates from other GitHub users for your website, e.g. jekyll themes
  • GitHub pages are free, fast, and easy to build, but limited in use of subdomain or URLs.

Confluence Wiki

  • CyVerse is paying for Confluence access.
  • Integration with other platforms like Jira.
  • Scripting in the Confluence Wiki is different than other platforms and may be less reprodicuble.

Build your own Website

Bookdown

  1. Install R and RStudio
  2. Install Bookdown package
install.packages("bookdown", dependencies=TRUE)
  1. Open the Bookdown demo and get started

GitHub Pages

  1. Create a GitHub account
  2. Clone the repo https://github.com/username/username.github.io
  3. Create an index.html
  4. Push it back to GitHub

CyVerse Confluence Wiki

  1. Create a CyVerse Account and log into https://wiki.cyverse.org
  2. Create a a new Blank Page
  3. Set permissions to share or make private

Methodology

Protocols.io - collaborative platform and preprint server for: science methods, computational workflows, clinical trials, operational procedures, safety checklists, and instructions / manuals.

QUBES - community of math and biology educators who share resources and methods for preparing students to tackle real, complex, biological problems.

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