PeerJ/[email protected]

Create, edit and (optionally) display a journal article, entirely in GitHub.

In contrast to the more traditional process of submit > peer review > publish at PeerJ, or even the less formal preprints at PeerJ Preprints or arXiv, Paper Now is an experiment to see where the future may go with scholarly communication. Initially, it may be that co-authors collaborate either privately or publicly on GitHub and then proceed to submitting to PeerJ or other journals for formal peer-review or preprinting. Or perhaps this is where the traditional medium of publication begins to diverge. There is no end goal other than to see what the academic community wants, which is why this is completely open to fork, extend, and build upon.

via PeerJ/paper-now.

Research Workflows and Tips (Primarily Oriented at Academics)

Liz recently had a conversation going on Facebook where some academic workflows came up. This is the sort of thing I love to read and then run my mouth about, particularly about software and methods of organizing the things that end up getting collected because I think it’s especially relevant to the ABDs.

I had some bookmarks on Pinboard that I hastily shared but I wanted to grab a few more things and put together a more tailored list.

Caveat: Since she and I both are firmly ensconced in the Apple Family, most of these are directly related to iOS and OS X software and I will make no apologies for that. There are many exceptional options for research and organization of information that favor OS X and iOS, and that’s where I spend the majority of my time so my sources are slanted that way.


The problem I had in putting this list together is that in some cases my bookmarks are a few years old, and things move and change quickly. Because of technology being such a fast-moving target, some of this will be a little different (or a lot different), but this shouldn’t be too distracting since, as best I can tell, most academic researchers commit to something and don’t fiddle with it nearly as much as I do.

General Workflows and Notes for Researchers and Academics

“There’s more than one way to skin a cat, and more than just a few tools for creating a paperless workflow for academic research and writing. I’ve noted some of the possibilities on the Affordable Mac apps for academic tasks page.”

Goes into some detail with various tools like Sente and DEVONthink, including the workflow they use for research, drafting, and polishing their work. Scrivener fan, too.

Luc Beaulieu

The e-Office series has some interesting workflow and notes relevant to academic research.

He’s also got some interesting Academic templates for DEVONthink Pro.

More about DEVONthink

I love DEVONthink Pro Office so much I want to marry it. Some notes I’ve found dealing specifically with DEVONthink are bound to happen. Luc’s templates are interesting but I’ve got tons of links!

DEVONthink is great at a lot of things, but honestly I don’t find it that exceptional for collecting β€” especially when I’m away from the computer. I prefer Evernote for that sort of thing.

Evernote Stuff

Rabbit-hole warning: Numerous outbound links here for other workflows

Sidebar: the Creating Personal Flow article on doing research lead me to a neat post about Commonplace Notebooks, which LL may like.


Thoughts and observations on software and workflows for more-productive academics.

Sidebar: I must tell you that I love Ulysses 3 and use it for writing projects all the time. It’s pretty awesome.


A lot of good notes about Scrivener but other interesting tidbits as well.

Academic workflows: revisited

It’s been a year since I wrote this post on academic workflows. The way I work has changed a bit since then – some apps have gone out, some have been added, and the relationship between some of them have changed, primarily affecting my literature review work flow. Here’s a little post on my current set up.


Fuck this shit, I’ll use paper

Go see my friend Patrick, and do not pass Go and do not collect the USD$200. You won’t need it anyway. Paper based markup systems!


My more complete archive of things I scrape away for later is pretty large, but some especially relevant items include but are not limited to things I tag as:

You’ll notice that many of these use tags for platform, e.g. iOS and OS X.