Markdown is a set of simple rules for writing text documents. Benefits include:

  • Plain text (future proof!)
  • Simple syntax, human readable
  • Wide community support and usage (e.g. GitHub, Tumblr, etc) by both bloggers and programmers
  • Supported by wikis (like MediaWiki) and many tools (see below) for producing content rich in links, graphics, tables, references, and more.

Writing for the web, not the desktop

All the content we now produce lives mostly on the web and sometimes on paper. So when it comes to designing and creating content we should move away from the world of 'paper document' layouts -- i.e we should stop forcing our initially created content into 8.5" x 11" or A4 page layouts. Instead, write documents (mixed with text, images, links, etc) with a simple set of structured rules (e.g. Markdown) which then allows for flexible conversion downstream into multiple types of documents: html, pdf, Word, etc.

Why markdown

Markdown tools

  • Multimarkdown is an extended version of markdown with nice citation and table support. Very nice for academic writing needs.
  • pandoc Universal document converter to/from different formats. For example markup languages (e.g. Markdown, MediaWiki, reStructuredText), LaTeX, html, LibreOffice, Microsoft Word...
  • github, jekyll, octopress: version control + collaboration, site generation, content management.
  • Many easy to use GUI apps exist for rendering Markdown on OSX, iOS, Android, Linux, Windows
    • Marked is one. Powerful and super flexible markdown/multimarkdown document previewer/exporter. Highly recommended if you are on Mac OSX.
  • App called Drafts featured at lifehacker for iOS. Powerful and flexible. Also simplenote, nvAlt for Mac, resophNotes for Windows

Additional tools workflow examples:

Dropbox CMS

Notes from an article on lifehacker on dropbox public website cms services.

With all these services they are best for small websites, not for big organizations or ones with lots of page hits as there is a dropbox limit per day and your account can get suspended.

  • Pancake
    • Preview common files like word, pdf documents right in browser
    • works with html, js, css, and plain text
    • 'free to sign up'
  • DropPages
    • markdown friendly
    • content gzipped and cached for best performance possible.
  • VoodooPad
    • Personal wiki
    • MacOS and iOS
    • tons of export options
    • sketching
    • unix shell scripting executiable
    • markdown friendly
    • project management

Lab notebooks in markdown

Open science initiative using git, github, R, knitr. Git based distributed version control is key to this sort of open project (software - science - data - documentation - manuscript) workflow. A more technical explanation of git magic.

Since a large number of scientific projects these days require substantial data analysis with interactive programming languages like R and python, mixing a structured markup language like markdown with the program interpreter is a very powerful way forward to helping achieve truly reproducible research (together with version control). Tools like jupyter/ipython notebook, Rstudio, and ropensci do exactly this and can be very helpful in this regard.

Here is an example lab-notebook from C. Boettiger with [github project hosting]((

nvAlt git selective note sharing

Markdown to html5 presentations


Highly technical GitHub dwellers have long used HTML5 presentations like Impress,js, Reveal.js, and Google’s HTML5 Rocks Presentations to impress fellow hackers with lean, well designed code and hand-tooled design.

Some are trying to emulate the non-linear prezi format. Some give traditional slide based formatting to markdown documents.


reveal.js download latest release


Reveal.js example

Define slides in index.html using external markdown. Notice the separator could be changed to something else, like a markdown hr: "^\n---\n"

<section data-markdown=""  

From reveal.js github readme

Some reveal.js features, like external markdown and speaker notes, require that presentations run from a local web server. The following instructions will set up such a server as well as all of the development tasks needed to make edits to the reveal.js source code.

Install Node.js

Install Grunt

Clone the reveal.js repository

$ git clone

Navigate to the reveal.js folder

$ cd reveal.js

Install dependencies

$ npm install

Serve the presentation and monitor source files for changes

$ grunt serve

Open http://localhost:8000 to view your presentation

You can change the port by using grunt serve --port 8001.

R html presentation solution Rmarkdown, Rpubs, Rstudio, github, dropbox

Built by Slidify. Styled with Bootstrap. Hosted on GitHub. Icons from Font-Awesome. Web fonts from Google. Inspired by Ruhoh

Usage example

install_github('slidify', 'ramnathv')
install_github('slidifyLibraries', 'ramnathv')

Then edit front-matter:

Title: Slidify Demo
Subtitle: HTML5 slides from R markdown
author: name
job: R hacker

Then make slides after ln 19 --- .class #id:

## Slide 1

Animated list
> 1. Point 1
> 2. Point 2
> 3. Point 3


## Motion chart

```{ r echo = F, results = "asis", message = F}

M1 = gvisMotionChart(fruits, idvar = "fruit", timevar = "year')
print(M1, tag = "chart")

Then click knit HTML and it will bring up an html preview.

Can add a line in the front matter for posting to github repo:

mode   : selfcontained # {standalone, draft}
  user: ramnathv
  repo: slidifyDemo

Then click knit HTML again.

Then publish from Rstudio command line to github:

publish('ramnathv', 'slidifyDemo')

Or delete the mode and github lines in the header and add:

mode: standalone

Then click knit HTML again.

Then you can click the publish button in the html preview window and it will let you upload documents to Rpubs and enter document details.

More R markdown awesomeness

The rpubs site is a place to publish R documents. Some people have released reports here, small starting community but mostly looks like nice resource for examples.

Example report of politician voting on defense bills with open data set

Example of network visualization in R

googleVis package examples

R markdown

R markdown notebook

Rstudio googleVis example

2013-08-20 14:18:19


Fruits dataframe

> Fruits
	    Fruit Year Location Sales Expenses Profit       Date
	1  Apples 2008     West    98       78     20 2008-12-31
	2  Apples 2009     West   111       79     32 2009-12-31
	3  Apples 2010     West    89       76     13 2010-12-31
	4 Oranges 2008     East    96       81     15 2008-12-31
	5 Bananas 2008     East    85       76      9 2008-12-31
	6 Oranges 2009     East    93       80     13 2009-12-31
	7 Bananas 2009     East    94       78     16 2009-12-31
	8 Oranges 2010     East    98       91      7 2010-12-31
	9 Bananas 2010     East    81       71     10 2010-12-31