Skip to content
Martin Fenner edited this page Jun 4, 2013 · 29 revisions

Workshop "Markdown for Science"

On June 8th, Martin Fenner and Stian Haklev are organizing a one day workshop at the Public Library of Science HQ in San Francisco. Spots are limited so register early.

If you are attending, please list yourself on people-attending with a bit about yourself, and your ideas/wishes for the workshop.

Some of the potential outcomes of the workshop include:

  • Notes from discussion about the suitability of Markdown for scientific authoring (different stages, disciplines, etc)
  • Comprehensive list of tools/initiatives
  • Notes from discussion about collaboration/synergy between tools
  • List of interesting examples/showcase (GH repositories etc)
  • List of "barriers", "obstacles" etc
  • Notes from discussion about way forward, applying for grants, etc

Please add your ideas below.

CSS Styles

@swcarpentry

@_inundata If you can make it easy (really easy) to add CSS styles to pre blocks in Markdown, you'll be my new best friend...

Use case is adding <span class="highlight"> or <span class="comment"> inside an indented block that triggers <pre>.

Mix Markdown with LaTeX

Paul Groth

One thing to say is that I like how authorea.com lets you mix and match markdown with latex. So a couple things to think about:

  • how do I transition from markdown to latex (do I want to?)
  • how do you deal with style files?

Standard additional markup

Philip Lord

It would be good to have some discussion on additional markup that might be needed for science. For example, I use [cite]doi://10.1000/1.1.1.1[/cite] or [author]Phillip Lord[/author] to define the author, within my wordpress plugins.

It would be nice to have some commonality both in the syntax (for example, "shortcodes" as I have used here) and the vocabulary. Ideally, something that will work in Markdown, but also non-markdown text syntaxes or even in word.

The sweet spot for markdown in scholarly communication

Karthik Ram

Markdown's greatest appeal is its simplicity. Adding features to support more complex use cases could be very counterproductive and we would worse off than just using LaTeX. So what are some of the key features we would need to implement to make markdown a standard tool for scholarly communication? Might be worth spending some time generating such a list and possibly build some prototypes time permitting.

31 flavors is great for ice cream but not markdown

Karthik Ram

There are many flavors of markdown at this time. Creating yet another one does not really help. Could we look through existing implementations and identify key features that facilitate scholarly use? For e.g. GitHub has its own non-standard flavor but some of their features are perfect for use in peer-review. Could we combine useful features into a scholarly markdown flavor (ok 32 is not so bad because this one is going to be the best).

Challenges

Martin Fenner

What will it take for a critical mass of researchers to use markdown for authoring? I think the biggest challenge is usability - most researchers aren't interested in learning a markup language. We therefore need nice WYSIWYG editors along the lines of Google Docs, that it is markdown (and git) underneath should matter only for the technical implementation and a small group of geeks. The other challenge is features, but here users may be much more forgiving.

One possible outcome of the workshop for me is that we are better off using the existing tools from LaTeX to online editors working directly with HTML5, and that markdown doesn't really fill a need.


The event is supported by a 1K Force11 Challenge prize.

Please contact the organizers @houshuang and @mfenner if you want to give a presentation or demo.

Clone this wiki locally