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Source code and version history for my online lab notebook

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Octocat-spinner-32 _includes hide rdf button April 22, 2014
Octocat-spinner-32 _layouts tweaking software sidebar experiment April 22, 2014
Octocat-spinner-32 _plugins update documentation. travis integration complete, closes #112 April 15, 2014
Octocat-spinner-32 _posts draft design notes April 23, 2014
Octocat-spinner-32 assets draft design notes April 23, 2014
Octocat-spinner-32 projects comment out any use of mendeley_category_feed April 11, 2014
Octocat-spinner-32 software update links on software layout April 22, 2014
Octocat-spinner-32 .gitignore ignore key files April 12, 2014
Octocat-spinner-32 .htaccess keep a local copy of the .htaccess file March 05, 2013
Octocat-spinner-32 .travis.yml update key April 14, 2014
Octocat-spinner-32 404.html remove manual timestamp tag in favor of git modified based timestamp June 04, 2013
Octocat-spinner-32 CNAME added CNAME file for github-based hosting April 04, 2013
Octocat-spinner-32 COPYING Modified language refering to CC0 declaration, #110 November 26, 2013
Octocat-spinner-32 Gemfile fix open3 gem (no need to add it to gemfile) April 14, 2014
Octocat-spinner-32 Gemfile.lock test travis April 11, 2014
Octocat-spinner-32 Makefile travis integration testing April 11, 2014
Octocat-spinner-32 R.xml templates for landing pages #77 March 29, 2013
Octocat-spinner-32 README.md update documentation. travis integration complete, closes #112 April 15, 2014
Octocat-spinner-32 Rakefile open3 for on git push call April 14, 2014
Octocat-spinner-32 _config.yml toggle off pageviews since cannot deploy via travis April 15, 2014
Octocat-spinner-32 archive.html page layout is now the standard (instead of default, which is now mor… April 12, 2013
Octocat-spinner-32 atom.xml removed table that isn't rendering May 21, 2013
Octocat-spinner-32 blog.xml blog.xml created #99 June 14, 2013
Octocat-spinner-32 calendar.md remove manual timestamp tag in favor of git modified based timestamp June 04, 2013
Octocat-spinner-32 categories.html remove manual timestamp tag in favor of git modified based timestamp June 04, 2013
Octocat-spinner-32 community.md remove manual timestamp tag in favor of git modified based timestamp June 04, 2013
Octocat-spinner-32 favicon.ico favicon added April 12, 2012
Octocat-spinner-32 index.html update semantic data April 15, 2014
Octocat-spinner-32 lab-notebook.html comment out any use of mendeley_category_feed April 11, 2014
Octocat-spinner-32 networks.md added Google Author info for experiment, closes #93 October 14, 2013
Octocat-spinner-32 research.md tweak format April 14, 2014
Octocat-spinner-32 robots.txt robots.txt added. February 08, 2013
Octocat-spinner-32 sitemap.txt minor updates January 31, 2013
Octocat-spinner-32 tags.html remove manual timestamp tag in favor of git modified based timestamp June 04, 2013
Octocat-spinner-32 teaching.md update a few references and links October 18, 2013
Octocat-spinner-32 vita.html orcid id below modification date April 22, 2014
README.md
layout title
page
About this site

Build Status

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

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

Site configuration

Fill in all elements of _config.yml appropriately.

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. jekyll serve)

Custom Plugins

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:

Carl Boettiger ("Page publication date"), "Page Title", Lab Notebook, http://carlboettiger.info


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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