1 About

My text processor, labnotes was first written in summer 2011 as a LaTeX wrapper to generate documentation from arbitrary pieces of bash, python, c++ or R script, as a replacement for Doxygen, for book-keeping of stuff I wrote for research projects. Hashtag # was therefore the default choice to lead a regular line of text, or “comments” in between codes, as it conforms to many programming languages. It was then polished to produce more formal documents as I started to use it for homework, project reports, and random notes. It made life better documented and research projects more reproducible. In 2012 a few others in the lab began to adopt it for documenting a collaborative data analysis project, and within roughly a year the program was expanded to generate beamer sides and HTML files for sharing at seminars and websites. Support for a couple of wiki platforms was later added to write documentation for projects such as this, this, this, and this. In 2016, I put together a simple bookdown template and switched to it from dokuwiki for daily work. On the Tax day of 2016 I posted the source code to github.

I never tried to advertise labnotes because the syntax and features are entirely driven by personal taste (hashtags, to start with!) and the implementation is continuous accumulation of monkey patches to get jobs done in the middle of a busy day. Nowadays knitr + rmarkdown rules and most of us write Markdown text. Still, I hold on to it because it continues to serve me well as it has over the years, and I have the liberty to shape it as I see fit. If your day job shares a lot similarities with mine (do statistics and computational biology using multiple programming languages, mostly via non-interactive batch commands, on messy data), you might find labnotes a fine choice to keep your project organized.

For installation please visit http://github.com/gaow/labnotes.

A complete demo is still in preparation.