The amount of science published every day is massive, making it extremely difficult to keep up with literature in your given field. I used to rely on keyword searches and RSS feeds or email updates on specific topics ("microbiome", "bacterial vaginosis", "probiotics", etc.) but this becomes a chore to keep up, and missing a day or two leave you with dozens of emails to catch up with. Not only that, but each weekly update on a topic will consist of 50-80 article titles that you have to read and sort and determine which are relevant enough to follow up on. I stumbled across this article in Nature (How to tame the flood of literature, Elizabeth Gibney) outlining some of these issues and suggested solutions.
So *is* there a better solution? Maybe not a catch-all tool, but here are some tools and software that have helped me out.
Automated recommendation tools
Google Scholar (online)
Google scholar is my primary tool for searching and finding publications. Once you make a scholar profile (linked to your Google account), you'll get an automated list of your own publications and citations (see mine here), including some metrics on your citation rate. Once you have a profile, Google will automatically suggest publications that are related to your work (they appear under "My Updates"). I find these updates are the most relevant to my research and what I am interested in.
Additionally, you can save articles you find via Google Scholar to "My Library". This keeps a list with links to the articles, along with citation metrics and information. However, this does not replace a citation manager as there is currently no way to export your list of articles, or automatically insert citations into a manuscript.
PubChase (online)
This is a new tool I am using, but I already see the potential. Like Google Scholar, it uses information about what you've published, but with the addition of articles you've saved to your Library as a resource to recommend articles relevant to you. Your Library can be populated by uploading a BibTeX (.bib) file, which nearly any reference manager will export for you.
Pubchase has some other useful features I haven't yet explored. It automatically links your library entries to PDF files (where possible) so you can read papers directly from your account. They also provide tablet, mobile, and computer apps for OSX, iOS, and Android, allowing you to read and access your library from any device. You can also make your library public for other members to follow, or follow someone else's library.
Pubchase has some other useful features I haven't yet explored. It automatically links your library entries to PDF files (where possible) so you can read papers directly from your account. They also provide tablet, mobile, and computer apps for OSX, iOS, and Android, allowing you to read and access your library from any device. You can also make your library public for other members to follow, or follow someone else's library.
Reference managers
A reference manager is essential for writing a manuscript and keeping track of citations. I don't have a favourite yet, but here are a few I've tried and liked:
Papers (Mac and iOS only; $)
An app you can install on your Mac and iPhone/iPad to access and view citations, and make notes and mark up PDF articles. It had a nice interface, and easily links to most word processing software (citations can be added to Word, plain text apps, Google Docs, etc.). The one major downside is this software has a cost, although there is a student discount rate.
Zotero (Mac, Windows, Linux; free)
Cross-platform, and free. Does the job, but the interface is not as clean as I'd like (seems a little 90s Windows-esque). Ability to insert citations and build reference lists for most document types.
Mendeley (Mac, Windows, Linux, iOS, Android; free)
Another nice looking application. It manages papers and citations. Has more functionality than I need though, and I find myself lost in menus sometimes. Seems to currently only support adding citations and building reference lists in Microsoft Word documents.
Other tools
Evernote (Mac, iOS, Windows, Linux, Android; free)
A multi-multi-purpose digital notebook. I use this for everything in my life, and it has become my digital lab book. You can add notes, PDFs, images, code, basically anything you want. You can compile notes into notebooks and tag topics. You can share with your workmates. It basically keeps my scientific life organized. Did I mention its FREE (I've found no need to pay for the premium subscriptions).
Blogs and social networking sites
Another source I use to keep up-to-date. A number of researchers maintain blogs with current information about their research or research in the field. I recommend using an RSS reader to receive the posts as they become live. Some I recommend:
CommaFeed (online)
Feedly (online, and available apps)
Also, the current Safari and Chrome browsers have RSS functionality built in.
Other sources include Facebook, Twitter, ResearchGate, and Google+. I find it's only useful to follow these if you are already an avid user. It's not feasible for me to check with every social networking site every day, and so I don't rely on these to keep up.
In case you are interested, here are some of the blogs I follow:
Not Exactly Rocket Science (Ed Yong)
Microbiome Digest – Bik's Picks (Elisabeth Bik)
Simply Statistics (Jeff Leek, Roger Peng, and Rafa Irizarry)
Bits of DNA (Lior Pachter)
Musings from an unlikely candidate (Dave Tang)
What You're Doing is Rather Desperate (Neil Saunders)
Please comment below on any other software tools that make your research life easier!
