Welcome to my online open lab notebook; home to all my research scribbles. This README documents the technical information about this site. If you’re looking for more about what this open lab notebook is about and why I keep it, consider starting with this introduction, or more about me.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or the University of California.
Site Features & Credits
- Colors and syntax highlighting with Solarized
- Crisp equations rendered in Mathjax
- Reproducible code execution with knitr
- CSS based on twitter bootstrap
- Scalable css icons from FontAwesome
- Static site generation with Jekyll
- Markdown parsing with pandoc
- Twitter, Mendeley & Github custom plugins
- Site and source code hosting on Github
- Uptime monitoring from my.pingdom.com; see status report
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 github.com/cboettig. 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 developed for my own needs and may be difficult to adapt directly to another purpose. If you are new to Jekyll, consider starting with a basic Jekyll template such as jekyll-bootstrap which will be considerably easier to adapt than working from this repository directly.
Clone the site source-code from github:
git clone https://github.com/cboettig/labnotebook.git
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 bundle install
Fill in all elements of
API key configuration
Several of my custom plugins require authentication credentials to the relevant API, which are not included when forking this public repository, for obvious reasons. These credentials should be stored as secure YAML files in the project source directory, and added to both
.gitignore and the
exclude list of
_config.yml. Currently credentials are only used for the Twitter and Google Analytics plugins. See the headers of these plugins for more documentation.
Building the site
To build and deploy the site simply run
bundle exec rake site:deploy
or to build locally use the standard Jekyll commands (e.g.
I have written a series of custom Jekyll plugins using these gems. See the header comments of each plugin for more details on their configuration and use. Most are written explicitly for my notebook and may require tweaking for general use. Plugins are frequently under development.
Copyrights & License
All original content is placed in the public domain by Carl Boettiger to the extent possible under law by the Creative Commons Zero declaration, CC0. Plugins are also provided under the MIT license. 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). Please cite or attribute this work as:
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.