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Source code and version history for my online lab notebook
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About this site

Site Features & Credits

Notebook Archiving & Data Management

The lab notebook is written and maintained in plain text (UTF-8) using markdown. All files are kept in a version managed repository system using git, which provides unique SHA hashes to protect against corruption. Synchronized backups of the git repository are maintained on both local and remote servers (RAID 6) to protect against hardware failures, as well as on the public international software repository, Github Version history preserves a time-line of changes and protects against user error. Archival copies of notebook entries shall be published annually to figshare where they will be assigned DOIs and preserved by the CLOCKSS geopolitically distributed 12 node global archive.

Building from source

This site is built by Jekyll, a static site generator which creates html pages from markdown files. Here are the instructions for building the site from source, based on my Ubuntu 12.04 platform. Feel free to adapt this configuration to your own needs.

Clone the site source-code from github:

git clone

Install Ruby version >= 1.9

sudo apt-get install ruby1.9.1-full

Make sure the latest version is selected

sudo update-alternatives --config ruby
sudo update-alternatives --config gem

Install Jekyll and the dependencies needed for a few plugins.

sudo gem install jekyll feedzirra nokogiri twitter octokit pandoc-ruby

In the root directory of the project, run jekyll --server, if successfull, after a few seconds the site should be available by pointing your browser to localhost:4000. The additional gems are required for various plugins; see below for more information. Due to these additional requirements, this site cannot be automatically rendered on Github's pages. Compile the site locally and copy the html files in _site to the gh-pages branch of a Github repository for Github-based hosting.

Jekyll Dependencies

The site relies on following additional ruby gems (not available on the Jekyll copy provided on Github's gh-pages) to compile successfully.

Required Gems

  • feedzirra -- Grab and format rss feed information
  • nokogiri -- parse HTML and XML
  • twitter Ruby bindings to the Twitter API
  • octokit Ruby bindings to the Github API
  • pandoc-ruby Ruby implementation of pandoc markdown interpreter (an alternative to redcarpet2)

Note: Markdown is wonderful, but a huge headache due to it's many flavors. I began using redcarpet2 via the redcarpet2 plugin which powers Github-flavored markdown, but have exchanged this for Pandoc. Pandoc markdown relies on a logically consistent internal grammar (leave it to the philosphers to write mathematically rigorous parser), something the original and some adaptations seriously lack. On a pratical note, Pandoc is useful for it's wide support of conversion to other formats, including pdf and word docs for publication.

Third Party Plugins

Plugins are provided in the site source, so cloning this repository will give you a copy of them. The site uses the following plugins:


All original content is licensed by Carl Boettiger under the Creative Commons Zero license, CC0. This license is uniquely appropriate for data, code, and written content, and facilitates distribution & reuse. Please remember that attribution and citation are appreciated where appropriate as proper scholarly practice. (Newton, Darwin, and Shakespeare are similarly in the public domain, but you wouldn't plagiarize from them). Cite or attribute this work as:

Carl Boettiger (2012), "Page Title", Lab Notebook,

with appropriate page title and publication date as indicated. Greycite is an excellent online tool that can generate the citation information for any particular page given it's URL.

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