Each blog post is a Markdown file in blog/_posts/. File names have post date and a short title. The short title is used for permanent URL links, so must be unique to each blog post. For example: Posts have the following YAML top matter:

layout: post
title: Some thoughts on a GitHub of Science
author: Trevor Bedford
image: /images/blog/github_large.png

Tags layout, title and author are required, while image is optional. The author name should correspond to the team member title tag for proper linking of posts to authors. All blog images should live in images/blog/ and be referred as relative to the base directory, begining with /images/.


Each paper lives in papers/_posts/. File names, used to construct permalinks, are first author plus short (1-2 word) title, for example Papers have the following YAML metadata:

layout: paper
title: Canalization of the evolutionary trajectory of the human influenza virus
image: /images/papers/bedford-canalization.png
authors: Bedford T, Rambaut A, Pascual M.
year: 2012
ref: Bedford et al. 2012.
journal: "BMC Biol 10: 38."
pdf: /pdfs/papers/bedford-canalization.pdf
supplement: /pdfs/papers/bedford-canalization-supp.pdf

Tags layout, title, image, authors, year, ref, journal are required. Tags pdf, supplement, github are optional. The image should be a 120x120 pixel tile. All paper images and PDFs should reside in images/papers/ and pdfs/papers/ respectively.


Each project exists as a separate git repository. To add a project and have it automatically redeploy when the project’s GitHub repo is updated requires the following two steps:

1. Add the project to the Jekyll index

Open the file _config.yml and append the full repo name to the YAML projects listing. This should then look like:

  - trvrb/coaltrace
  - trvrb/stem
  - owner/project-name

where owner and project-name is specific to the new project. Commit this change to the blotter GitHub repo.

2. Set a webhook from GitHub

From the project repo, go to Settings / Service Hooks / WebHook URLs, and add to the list.


Each team member has a Markdown file in team/_posts/. File names are join date followed by first and last name, like YAML follows:

layout: member
title: Trevor Bedford
position: Principal investigator
handle: trvrb
twitter: trvrb
github: trvrb
image: /images/team/trevor-bedford.jpg
cv: /pdfs/team/bedford-cv.pdf

Tags layout, title, last name, position, handle, image are required, while twitter, github, cv are optional. The image should be a 260x260 pixel tile. All member images and PDFs should be placed in images/team/ and pdfs/team/ respectively.