Introduction

Why am I writing this?

Reading is a fundamental part of any scholarly work. Unfortunately how to find and organize relevant literature, and how to read a scientific paper are not topics that are commonly covered in graduate or undergraduate courses or workshops. Furthermore, technological stack changes quite rapidly, and over the past 5 years during which I was getting a PhD a few new tools came out and a few old ones became a lot better. Thus, I think that it’s a good idea to put some of my thoughts and practices into a note that hopefully will be of use to you.

Tech stack

• Google Scholar
  • A great search engine for sifting through academic literature
  • Most useful features are restricting search to specific years (great when you know that paper is by XYZ et al. 2009) and manual traversal of the citation graph
  • Obviously a paper will list its references inside the corresponding section, but Scholar let’s you go in the other direction looking up papers that cited selected work
• Google Scholar Button (browser plugin)
  • Lets you interface with Scholar database in one click from the current paper webpage, useful for searching “Cited by”
  • Allows creating a properly formatted reference in a variety of formats, BibTeX being one of the more useful ones
• Zotero
  • Zotero is a citation manager with a lot of features and plugins
  • Most useful plugins are web browser integration that lets you quickly add a paper into your collection of references and Google Docs and Word plugins that allow you to neatly interface with your collection and organize the references
  • Zotero allows sharing collections of references with other users which can be great for collaborative projects and new students continuing other people’s work
  • Zotero allows you to export references in BibTeX format, but I found this feature to be more cumbersome than manual compilation via Google Scholar button. That being said the one case where Zotero is likely to be more helpful is if you are exporting large number of references at once. This can come in handy when writing a thesis or a book that is based on several papers you have already wrote.
  • Zotero can also save PDFs of the articles you add to your collection, but I tend to find keeping PDFs in Zotero less intuitive than other organization schemes
• Google Scholar PDF Reader
  • At its best it turns all references in the paper into clickable links to Google Scholar which can speed up citation graph traversal
  • However, the tool is still experimental and sometimes has bugs in PDF parsing
  • Also the recent AI outline feature seems to be counterintuitive when compared to a regular section breakdown of a PDF
• Finder tags (MacOS)
  • Finder allows you to tag files with color (default), but it also enables custom tagging with descriptive keywords
  • While this approach is manual and can look messy, I find it work quite well for organizing my offline PDF library
• Notion
  • Sleek note taking app with a ton of features
  • I find Notion to be useful when organizing my thoughts on a broader topic when I might want to bring in links to multiple papers and work on a blog / research journal write up
• Google Slides / PowerPoint / Beamer
  • While I think it is unsustainable at scale, a good practice early on is to have a “flash card” template that you can fill out for papers you are reading on a particular topic; there are several template formats ranging from 1 to 3 slides, and this approach encourages you to think through each paper in a structured way.
  • A neat bonus of using slides for paper summaries is that eventually you will accumulate a set of brief points on a large corpus of literature allowing for more efficient review paper writing in the future

No longer part of the stack

• Notability
  • Over the past few years Notability steadily degraded from being an app worth getting the iPad for, to an app full of subpar features and hidden costs
  • I used Notability mainly to annotate papers I read (e.g. highlighting important parts, adding quick handwritten notes); However, I realized that I rarely go back to these annotations and other methods of organizing my notes are more efficient
  • I think Notability is still a decent tool to have if you have an iPad, but I think it’s overall priority has dropped below the recommendation bar

Finding literature

Good habits

• Once you find a paper, make a quick note (a phrase or a sentence) about why this paper (title/abstract) grabbed your interest. Most of the time you won’t read the whole paper right away, and even if you do it will likely be a quick skim. Keeping track of why a browser tab is open helps you streamline your reading experience.

Leveraging libraries

Using academic institution libraries deserves a separate section due to the impact it can have on expanding your search and retrieval toolkit, and due to the unfortunate fact that we often times overlook this resource.

• Often academic institutions you had been affiliated with (even temporarily) will allow you to retain credentials for digital access to their library systems. In many cases having several institutional library credentials will allow you to bypass paywalls on a much wider array of academic journals and books.
• Usually we think of libraries when we need to grab a particular book. If this book is relatively new it can be unavailable at the library. However, some libraries (including Rice Unviersity’s Fondren Library) have request forms which you can fill out to suggest book purchase. Over the past few years, this helped me fetch a fresh book on string algorithms, and a textbook for an introductory bioinformatics class.