Academic reading workflow

3.1 Active reading

Baldur Bjarnason, Neither Paper Nor Digital Does Active Reading Well:

Catching up on usability research throughout the years makes you want to smash your laptop against the wall in anger. And trying to fill out forms online makes you scream ‘it doesn’t have to be this way!’ at the top of your lungs. […] The same applies to reading software. When you read up on research and papers on skills development, memory formation, and active reading, frustration with existing tools inevitably follows.

At least with paper, we can teach people to hack their tools—extend the printed book with post-its, commonplace books, bookmarks, and inline annotation. Doing the same in digital is incredibly hard without programming skills […] or expensive tools, even when the closed silos allow it. […]

The cognitive effort to actively and intelligently read a text in depth is, if not equal to, then on the same order of magnitude as the effort to write about a complex subject.

But we only have full-featured tools to help us with writing. Ulysses, Tinderbox, Scrivener etc all make managing and writing a complex writing task much easier. Even code-oriented text editing workflows […] with their steeper learning curves are a major improvement over paper-based writing workflows.

We can also use paper-based writing tactics in tandem with the digital ones, to the point of going back and forth between the two. You can’t do the same easily with reading.

Which leads us to the current situation: our ability to handle complex writing tasks is increasing while our default reading toolset is stagnating at best.

He ends up giving an extensive advertisement for liquidtext, an iPad app with lauded UI development, which looks nice. If you have an iPad.

4.1 Collective annotation

A neat one is pubpeer’s overlay for web browsers which opens a window into the sometimes-acrimonious academic critique world. (Their peeriodicals system might take this to a new level within teams.)

Hypothes.is

Select text to annotate. Add tags and post publicly or save privately.

Reply to or share any annotation. Link to notes or whole pages.

Annotate together in groups. Collaborate privately with others.

Search your notes. Explore all public annotations and profiles.

They have documented a recommended workflow.

Vortimo

is software that organizes information on webpages that you’ve visited. It records pages you go to, extracts data from it and enrich the data that was extracted. It augments the pages in your browser by allowing you to tag objects as well as decorating objects it deems important. It then arranges the data in an UI. Vortimo supports switching between cases/projects seamlessly. You can also generate PDF reports based on the aggregated information and meta information.

Vortimo can be used by anyone that uses a browser to research a topic. This includes investigators that are profiling individuals or companies, intelligence analysts using open source intelligence (OSINT), IT security personnel or even academics doing domain specific research. Vortimo collects and organizes information that came from your browser — so it does not matter if you’re browsing the web, using social networks or visiting your company’s intranet.

pdfx (source) claims to:

• Extract references and metadata from a given PDF
• Detect pdf, url, arxiv and doi references
• Fast, parallel download of all referenced PDFs
• Output as text or JSON (using the -j flag)
• Extract the PDF text (using the --text flag)
• Use as command-line tool or Python package
• Works with local and online pdfs

Fermat’s Librarian is

A Chrome extension that enhances arXiv papers. Get direct links to references, BibTeX extraction and comments on all arXiv papers.