DEPRECATION NOTICE

This is an old version of the website. If edits are needed, please edit this content:

https://github.com/sbgn/sbgn.github.io

SBGN Homepage & Development Wiki

This repository contains the code for the SBGN homepage available at
http://sbgn.github.io/sbgn or http://www.sbgn.org

and provides access to the developer Wiki at
https://github.com/sbgn/sbgn/wiki

Website Development

This website is a GitHub Pages Jekyll-based website. GitHub Pages are public web pages for users, organizations, and repositories, that are freely hosted by GitHub. When commits are made to this repository files are automatically built into a static website by Jekyll and changes appear on the live website quickly. The main syntax of the website is Markdown (a Wikipedia MediaWiki-like syntax) that is described better in links below.

Contributions and changes can be made in several ways:

1. Downloading files using Git and pushed back to this repository directly or via pull requests. Please get in contact with one of the SBGN editors if you need commit permissions.
2. Through the online GitHub Editor by clicking the Edit menu on any .md file.
3. Submitting an issue on our issue tracker.

Website Structure

Menu Items

Menu items https://github.com/sbgn/sbgn/blob/gh-pages/_includes/header.html

Earlier menu items are stored in
https://github.com/sbgn/sbgn/blob/gh-pages/_data/menu.yml

Rendered by the template
https://github.com/sbgn/sbgn/blob/gh-pages/_includes/header.html

Pages

All pages are stored in
https://github.com/sbgn/sbgn/tree/gh-pages/docs

and rendered by the template
https://github.com/sbgn/sbgn/blob/gh-pages/_layouts/default.html

Homepage

The main landing homepage (index.html) is rendered by this Markdown file:
https://raw.githubusercontent.com/sbgn/sbgn/gh-pages/_includes/index.md

Using Markdown

• Jekyll Kramdown Notes: http://mindspill.net/computing/web-development-notes/kramdown-notes/#tables
• GitHub Jekyll Notes: https://github.com/blog/2100-github-pages-now-faster-and-simpler-with-jekyll-3-0
• Markdown syntax in GitHub: https://guides.github.com/features/mastering-markdown/

Notes on GitHub (Troubleshooting Jekyll)

Conflicts

If you edit a page in your browser it might happen that you see the message "### has committed since you started editing. See what changed" while committing. This means someone else was editing the page at the same time and did a commit prior to your commit. To avoid data loss, copy your changes to an editor, updated the page you were about to edit, insert your changes, and do a commit.

Editing index.(md,html)

The index.md exists in the _includes folder.

Example Page Front Matter

Example Jekyll Front Matter necessary to render a page correctly:

---
title: A Human Readable Title
layout: default
permalink: /a_human_readable_title
---

NOTE: There is only one layout (i.e. default)

Images

Example image code:

![alt text](/images/foo.png)

NOTE: If you need to directly link to an image found in a GitHub repository use the following URL syntax:

https://raw.githubusercontent.com/sbgn/glyph-files/master/simple_chemical/Symbol-simpleChemical.png

Tables

• There must be an empty line below the table

Linking

• File names should be at least 3 characters (WRONG: faq, RIGHT: faqs)
• Given the relative path in the Markdown links

Example

• You need to give relative path

• Example: faqs.md is in docs/ and pd.md is in docs/faq/

  We would like to provide a link of pd.md page in faq.md

  The path of the link to give: faq/pd

• The syntax for creating a link is available here.

Redirects

In some cases, links will need to be redirected from a former location. This can be done with the following lines. The example redirects http://sbgn.github.io/sbgn/LibSBGN to https://github.com/sbgn/sbgn/wiki/LibSBGN

---
redirect_to: https://github.com/sbgn/sbgn/wiki/LibSBGN
---

Run Site Locally with Docker

Get Docker

https://docs.docker.com/engine/installation/

Get Docker images

Jekyll with GitHub plugins

docker pull cannin/jekyll:gh

HTTP Webserver

docker pull cannin/jekyll:gh

Run Docker with Jekyll

docker stop jekyll; docker rm jekyll; docker run --rm --name=jekyll -p 4000:4000 -v=$(pwd):/src -it cannin/jekyll:gh bash

Build in code root directory

bundle exec jekyll build --destination sbgn

Run webserver

docker stop tmp; docker rm tmp; docker run --rm --name tmp -p 8080:8080 -v=$(pwd):/src -w /src -t cannin/nodejs-http-server

Access site

http://localhost:8080/sbgn/

Template Documentation

https://github.com/orderedlist/minimal