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It is Wednesday Hyperlinks Of My Preference time, for the first time.

Here are some of the links around the webs I found interesting or useful. Let's WHOMP.

Popular Science

Some of my favourite popular science writing from last week:

  • The Worst Places To Get Stung By A Bee: Nostril, Lip, Penis - By Ed Yong. The story of a very dedicated scientist out to answer the burning (make that stinging) question of where is the most painful place to be stung. The target audience appears to be humans but this information would be very valuable for angry bees. Let's try and keep this from falling into the wrong tarsi.

Useful Tools

Here are two online writing tools that may help you if you are writing a paper or a thesis chapter. I think both of these have great potential but neither quite have all the features to make them a killer app just yet. Using the cloud to do writing has many advantages, including automatic backup, the ability to work on a document from anywhere, and ease of collaboration and sharing of the final result.

Both of these tools are primarily based on markdown, and could be a good way for anyone who is thinking of picking it up to give it a try in a nice looking GUI system. If you don't know what markdown is, @_inundata has some good resources here. Also, @polesasunder has an interesting post on a small part of his experience with markdown (I promise you, it is not just for hipsters). Here are a few pros and cons of what I think are the two most promising cloud writing apps I've tried.

Authorea

Pros:

  • Version control using Git (awesome!)
  • Easily rearrange paragraph order
  • Automatic citation and bibliography generation by simply pasting DOI numbers into the text (Love this feature!)
  • Integration with iPython Notebooks for on the fly or interactive visualization
  • Writing with either markdown or Latex
  • Unlimited public documents. Free for papers being published open access (Love this!)

Cons:

  • Only one private document with a free account; you have to pay for more.
  • Interface not keyboard friendly, which makes it a bit clunky.
  • Limited export formats (just PDF, markdown and Latex), no Word export could be a deal breaker for some people.
  • Most importantly for me now, no R integration (they say they are working on it!).

Overall, once R integration is achieved this could make me think about switching from my current solution using RStudio with rmarkdown, and GitHub for syncing and version control. More about this system in upcoming posts!

Gingko App

This is still in early beta and has much fewer features than Authorea at the moment, but what makes it stand out is its delightful fluidity.

Pros:

  • Incredibly elegant, everything can be done with the keyboard without any complicated hotkeys to remember.
  • Fully hierarchical structure that unfolds across the page, allowing you to outline and write your content in the same place. They call it tree-based word processing. It is quite stunning.
  • Styling with markdown and Latex.
  • Export to useful formats including markdown, PDF, html, and importantly Word.
  • This video shows some of these nice features:

Cons:

  • Adding figures is not simple as you need the image to already be online and have a URL
  • No automatic citation system yet (they say they are working on it).
  • Free account is limited to only three documents (which they call trees), for more you must pay

Overall, I love this app, and I think once I got the hang of it, it could be that rare software tool that actually aids the flow of ideas, rather than disrupting them. For now it is great for the early stages of writing where you are trying get the structure down, but it also lets you add in content as you go, so you can go wherever your mind takes you. Perhaps after this stage, the document can be exported to another program for the finishing touches such as citations.

Both apps allow multiple users to work on a document at the same time, so they are both fantastic for collaboration. To summarize, Authorea has great technical sophistication and some real sweet features, but a somewhat clunky interface (but its still not bad at all), whereas Gingko App makes up for its lack of bells and whistles with elegant simplicity. I am looking forward to see whether the upcoming planned features for these apps will make one of them the killer writing app I've always been looking for. I hope you give these a try, because I want these tools to be a success and have the chance to reach their full potential.




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Russell Dinnage


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MetaEvoPhyloEcoOmics

Open science journal about ecology, evolution, data analysis, and visualization.

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