Bio-IT Community Docs
Documentation of the EMBL Bio-IT Project. Bio-IT was established to build and support the computational biology/bioinformatics community at the European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
See the site at grp-bio-it.embl-community.io/docs/.
These docs provide information and practical guides about the community, the project, and their activities. The site was originally developed by Toby Hodges under the Center for Scientific Collaboration and Community Engagement's concept of a Community Playbook, as part of the CSCCE Community Engagement Fellows Program 2019 (CEFP2019).
Build info
The site is built with Jekyll and GitLab Pages, using the Just the Docs theme. Pages are served via Continuous Integration on the EMBL GitLab instance.
To build these pages locally,
clone this repository,
install Jekyll and Bundler,
then run bundle exec jekyll build from the project root directory.
To view/test changes locally before pushing,
run bundle exec jekyll serve
point your favourite web browser to http://localhost:4000/docs/.
Site structure & links
Pages are added to the site as Markdown files. To be rendered on the site, a page must begin with front matter:
---
title: Example # required
layout: default # required: change this to use a different layout for the page
description: "Documentation of the EMBL Bio-IT Community." # required
permalink: / # required: defines URL path to page
parent: Page Parent # optional: used to specify page under which current page should be listed in navigational structure
has_children: true # optional: used to define navigational structure for tables of content & menus
nav_order: 0 # optional: used to control the order in which pages are displayed in the navigational structure
tags: ["example"] # optional: provide one or more tags for the page, in an array. These tags will be used to help readers find pages/info relevant to their needs
---Markdown files should also end with the {% includes links.md %} tag,
to ensure that links are rendered correctly (see below).
In lieu of a more elegant solution,
the CI pipeline will throw an error if this tag is not found
within the last five lines of a Markdown file in the repository
(excluding README.md files or those starting with _).
Links to external pages should be written as
[link text][link-target]with a corresponding entry added to _includes/links.md in the format:
[link-target]: https://link.target/To ensure correct link resolution, links to other pages within the site should be written as
[link target]({{site.baseurl}}link/target/)Timestamps
There are few things more annoying than unwittingly using outdated information.
To display a "This page was last updated on YYYY-MM-DD" timestamp to a page
(with the date corresponding to the last time that specific page was modified),
add the path to the desired page(s) to _timestamp_files.txt.
Contact
If you have questions about these pages, about our community, or about the EMBL Bio-IT Project in general, please contact bio-it@embl.de.