Source code and version history for my online lab notebook
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Latest commit 6afd2e4 Mar 16, 2016 @cboettig custom sass
Failed to load latest commit information.
_includes fix typo Oct 28, 2014
_layouts fixing a few validation errors Aug 4, 2014
_plugins update sha and Dockerfile Oct 28, 2014
_posts update dockerfile Mar 16, 2016
assets custom sass Mar 16, 2016
.dockerignore update Dockerfile to test out with servr Dec 31, 2014
.gitignore debugging build.R Dec 31, 2014
.htaccess keep a local copy of the .htaccess file Mar 6, 2013
.travis.yml toggle off travis deploy in favor of local deploy (gets sha hashes co… Dec 31, 2014
404.html remove manual timestamp tag in favor of git modified based timestamp Jun 5, 2013
COPYING Modified language refering to CC0 declaration, #110 Nov 27, 2013
Dockerfile update dockerfile Mar 16, 2016
Gemfile update Sep 3, 2014
Gemfile.lock experimenting with revised Dockerfile build Dec 30, 2014
Makefile tidy up _config Jan 1, 2015
R.xml update Dockerfile, drop non-existant layout on atom feed Sep 3, 2014 update README and index, drop hastingsfest slides Dec 30, 2014
Rakefile use rsync instead Dec 30, 2014
_config.yml Merge branch 'master' of Jan 1, 2015
archive.html page layout is now the standard (instead of default, which is now mor… Apr 12, 2013
atom.xml update Sep 3, 2014
blog.xml update Sep 3, 2014
build.R tidy up _config Jan 1, 2015 remove manual timestamp tag in favor of git modified based timestamp Jun 5, 2013
categories.html tweak category layout Jun 18, 2014 remove manual timestamp tag in favor of git modified based timestamp Jun 5, 2013 still tuning local build and deploy Dec 31, 2014
favicon.ico favicon added Apr 12, 2012
index.html update README and index, drop hastingsfest slides Dec 30, 2014
lab-notebook.html don't use fluid/full-width container May 5, 2014 update some icons, add impactstory and G-scholar to vita page May 13, 2014 update posts, set plugins to use env vars, add Dockerfile Aug 29, 2014
robots.txt robots.txt added. Feb 9, 2013
sitemap.txt minor updates Jan 31, 2013
tags.html fix tag page layout Jun 18, 2014 update a few references and links Oct 18, 2013 update vita Sep 19, 2014

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About this site

Build Status

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

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 file loss. 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

NOTE: 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.

The site's .travis.yml file contains the recipe to build this site from scratch on Travis-CI, which is how the site is currently deployed. As such, the script will always provide the current steps necessary to get the site to build (Travis-CI is based on a Ubuntu 12.04 image; these directions can be adapted as needed).

This site repository also now includes a Dockerfile for generating a portable docker container to generate the site.

A separate Dockerfile for building boostrap 3.1.1 CSS can be found in the assets/_bootstrap-3.1.1 directory.

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.

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,

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.