THIS IS THE OLD COURSE WEBSITE

For EEOB/BCB 546, go to the new repository https://github.com/EEOB-BioData/EEOB-BCB-546

EEOB/BCB 546X Course Website

This repository hosts the website for the graduate course "Computational Skills for Biological Data". This is a static site built by Jekyll and based on the Millidocs Theme.

Editing and Building the Site

To edit this site, you must first clone this repository

git clone git@github.com:EEOB-BioData/EEOB-BCB-546X.git

Then, change directories to EEOB-BCB-546X.

cd EEOB-BCB-546X

To build the site, you must have Jekyll installed. If you have Jekyll, you can install the Millidocs bundle:

$ bundle

Or install it yourself as:

$ gem install millidocs

Now you should be able to serve the website on your local machine using Jekyll:

bundle exec jekyll serve

This will generate the whole site so that you can view it on your own machine at http://127.0.0.1:4000/.

Now if you make changes, you will be able to preview them before pushing the source to the remote host on GitHub.

Troubleshooting

If you get errors when running bundle exec jekyll serve this may be because you need to update installed gems or Gemfile snapshot. To do this first update your gems in the Gemfile:

bundle update

Then install any missing gems:

bundle install

You should be able to serve the site now:

bundle exec jekyll serve

Directory Structure and Making Edits

Most of the files in the site directory determine the style and layout of the pages. This Jekyll theme only supports page, which are all composed in Markdown and should be located in the top directory.

Additionally, there is a directory called slides, which is where we can post the lecture slides. We can simply link to these slides using their relative paths: [today's lecture slides](slides/today_lecture.html).

Updating for a New Semester

When starting a new semester, it's necessary to make changes to the site. Here are the steps:

• create a new GitHub repository for the course data files and documents, the format for naming this is BCB546X-FallYEAR
• create a new syllabus and place it in the repository above
• update the GitHub and Canvas links in _includes/navigation.html
• update the year in _includes/sidebar.html
• remove previous year's content in:
  • index.md
  • schedule.md
  • assignments.md
• correct the link to the syllabus on index.md
• update the link to the schedule on schedule.md

New Look

It is typically good to give the site a new look for each semester. This can be achieved by changing the theme (a lot of work) or changing the colors of the current theme (little work). Here are the colors we have used:

Fall 2018 Green Theme

• _sass/milligram.scss button background color #047900
• _sass/variables.scss navigation background color #C9E0C4
• assets/css/docs.scss link color #047900

Fall 2019 Blue Theme

• _sass/milligram.scss button background color #006878
• _sass/variables.scss navigation background color #AAD4E6
• assets/css/docs.scss link color #006878