plantgghlab.github.io

https://plantgghlab.github.io

https://plantgenomics.ksu.edu/liulab

Notes

• This site is generated with Jekyll. Documentation for Jekyll can be found here.
• The content of this site is generated from Markdown files. By default, Jekyll processes Markdown files using kramdown. Documents for the syntax understood by kramdown can be found here.
  • Another Markdown processor can be used instead by setting the markdown key in _config.yml (See also).
  • You can also use HTML file directly instead of Markdown.
• Jekyll uses the Liquid template language process Markdown/HTML templates.
  • In short, you denote variable with double curly brace (e.g. {{ var }}) and logic statement with curly brace percentage sign (e.g. {% if condition %}...{% endif %}).
  • For an example of Liquid in action, see people.md. For more details, see the official Liquid documentation.
  • Jekyll also provides a number of useful Liquid additions
    • Jekyll-specific filters
    • Jekyll-specific tags
• Files can specify data/metadata using front matter (a YAML block at the beginning of the file, delimitted by triple-dashed lines). For examples:

  ---
  title: Publications
  # by default, expand this many years/sections
  show: 3
  ---
  ...

• For more Jekyll resources, see here.

Some common tasks

Uploading static files

Static files such as images should be added under assets/. It is not mandatory but images should be put under assets/images/ for organizational purpose.

Adding a news item

• Create a new Markdown file under _news/ with the name following the format YYYY-MM-DD-optional-title.md, its contents should look something like this

  ---
  ---
  Something happened!

  • NOTES: the YAML header is required. Otherwise, the file is ignored by Jekyll.
• The date in the filename is used for sorting. By default, 10 most recent news items are shown. This value can be changed by editing the file _includes/recent_news.md.
• If the news item is associated with a website/study, you can provide either link or doi in the front matter block. An appropriate link will be appended automatically the news item. Example 1, and example 2

Adding a new lab member

Create a new Markdown file under _people/ with the name NN-name.md where NN is a number to determine sorting order. Higher value means listed first.

The content of the file should look something like this

---
name: Dr. Sanzhen Liu
position: Associate Professor
email: liu3zhen@ksu.edu
photo: assets/images/people/liu.jpg
---
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
culpa qui officia deserunt mollit anim id est laborum.

• position if unspecified, defaults to Undergraduate Research Assistant. This default value can be changed by editing _includes/person.md
• email is optional, only shown if specified
• photo if unspecified, a default avatar is shown
• After the front matter, an optional bio can be added as well

Adding a new blog entry

• Create a new Markdown file under _blog/ with the name following the format YYYY-MM-DD-optional-title.md
• NOTES Similar to news item, a front matter block at the beginning is required.
• To attach a photo to the blog entry, specify img: in the YAML metadata where to find the photo. See 2018-08-24.md for an example.

Adding a new publication

• Add a new entry in the YAML file _data/publications.yml
• A link to the publication will be appended if the optional doi key is specified.
• When a footnote is needed, use the normal Markdown syntax to write the footnote. But the footnote definition(s) should be placed under the footnotes key, like so

  - year: 2014
    pubs:
      - citation: "J Nestler, S Liu[^nestler], TJ Wen, A Paschold, C Marcon, HM Tang, D Li, L Li, RB Meeley, H Sakai, W Bruce, PS Schnable, F Hochholdinger, 2014 Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase. Plant J, 79: 729-740."
        doi: 10.1111/tpj.12578
        footnotes: |
          [^nestler]: Co-first author

Site-specific plugins

Jekyll plugins are written in Ruby. Some plugins specific to this site are found under _plugins/. For documentation on how to write a Jekyll plugin, see here.