Navigating the scientific literature - glasgowlab/home GitHub Wiki

Why read papers?

Lots of good reasons.

  1. Learning about recent work in your field
  2. Learning about work outside the field
  3. Contextualizing your project
  4. Writing your own papers
  5. Staying on top of new methods, datasets, and experimental approaches that could be useful to you now or in the future

How to read the literature

Because your reasons for reading might vary, there are different ways to approach papers.

  1. Skimming - sometimes it's not necessary to read the whole paper. You may just be interested in the abstract/methods section/figures and captions. In the end you consume 15-20% of the paper but come away with the main point.
  2. Deep read - consume the whole paper with a highlighter and notepad, trying to fully understand what the authors did to get to their conclusions. Google every word you don't know.

Keeping up with the latest developments

Once you build a muscle for it, scanning/reading papers is really fun. It should only take a few hours per week on average to stay on top of new papers in the field.

Build a routine

You can check out new research while you're riding the subway and drinking your coffee in the morning. One of the best parts of my week is Saturday mornings: I set aside a few hours to read papers in depth that I've been looking forward to in peace and quiet. Alternatively, I will sometimes use this time to read up on a topic I want to learn more about from older papers or reviews. It's not important when, where, or how you do it, but it is important to build a habit of reading the literature. A routine of some kind can help. I also enjoy sharing and discussing thought-provoking papers on our #interesting-papers Slack channel, which usually deepens my understanding of what I read.

Useful tools to alert you to new papers

  • RSS feed (e.g., Feedly; see these guides to building an RSS feed from the Fraser Lab)
  • Google Scholar updates: here is a resource on getting relevant papers from their automated recommendations
  • NCBI updates: set up custom filters and specify how frequently to receive the info
  • Social media: Twitter/X, BlueSky, LinkedIn
  • Podcasts
  • bioRxiv alerts: specifiy by subject area, collections, authors, or key words. I also typically scroll through the latest bioRxiv titles in the Biophysics or Biochemistry subject areas upon waking up a couple days a week.
  • our #interesting-papers Slack channel!

Managing references

As you grow your knowledge, it's important to keep track of what you learned and where you learned it in one place. Reference managers are super useful for this. Think of it like a virtual library.

There are many options: Zotero, Mendeley, Endnote, Papers, Paperpile, Scrivener... but in our lab we use Zotero for several reasons:

  1. Zotero allows us to share references in one place as a group. Folders improve organization. For example, Belen and Chenlin have a shared PFK-1 folder. Daniel and Kyle have a GPCRs folder. I sometimes make folders for specific grants. It's a good idea to make a folder early on for your thesis references. Folders are not, however, required to collate references as long as they are somewhere in the group library or in your personal library (which is not visible to the group unless you add it there also).
  2. Zotero is compatible with Google Docs, where we write papers/grants collaboratively, via Zotero Connector. There is an additional plugin to seamlessly handle moving references between Google Docs and Microsoft Word (or another word processor). Additionally, there are browser extensions for Chrome, Firefox, and Safari so that if you read something interesting, you can just click a button to save it to your Zotero library (and when clicking, you have the option to specify which folder in the library).
  3. You can annotate papers within Zotero, keep notes, and it will also store PDFs.
  4. It's easy to find stuff using limited information with the search function - like if you only remember the journal, first author's last name, year, or two words in the title.

Get started with using Zotero