Who ya talking about? Cite them! But not by hand! Use a citation manager (aka reference management software) like Mendeley if you don’t already – future you will thank present you if you do! (especially if you’re working on your thesis where you have hundreds!)

And, yes, I spent my weekend working on this because, weird as it may be, working on my thesis is the one thing that’s actually giving me joy in this stressful final stretch of my PhD journey – I think probably because it feels like the one thing I have some control over – and because it’s cool to see it come together! Citations and all!

note: This is one of those practical posts that some people will find helpful and some people won’t – or at least think they won’t – and those people have probably stopped reading already. But I’m going to go ahead and start off with explaining some of the basics of the terminology, etc. so everyone’s on the same page. And then, for those who stick around (or jump past that intro) I will talk about how to get your references to stick around – in one place, which is searchable, add- and remove-able and insertable! Because, although it is possible to manually make citations and reference sections, it’s definitely not practical! So there are lots of helpful tools often called “reference managers” like Mendeley (a free program I use), Zotero (also free), Endnote (not free), and Pages (not free). These keep track of all the papers, books, etc. you think you might possibly want to cite (or at least remember you read) in the future. They download all the information required for citing a work you tell them to (through a browser plug-in, title search, etc.). And then, later, when you ask them to, they’ll provide references formatted in the style you ask them to. 

There are also some website-only services like EasyBib, Scribbr, Bibliography.com, zoterobib, etc. that will give you basic citations (though often just in 1-3 basic formats). Those can be good for in high school or undergrad when you are just doing a class report with a small number of citations you’re probably only going to need to use for that one assignment. But once you’re doing your own research projects, it’s time for one of these more serious ones where you actually download software, so there’s a stand-alone desktop version (that works when you don’t have wifi) that actually saves everything for you and has way more functionality. These ones I’m talking about often also have browser extensions and/or web versions that sync to your desktop one. 

note: I still use EasyBib or one of those browser-only guys sometimes if I’m citing websites and/or news articles for posts and things, but not for my PhD research stuff 

So, let’s get on the same page (no pun intended this time) about what I’m talking about and why it’s so important. Then, I will introduce you to user-friendly software, and then show you a new thing I learned – making custom .bst files to use in LaTeX to get custom bibliography styles which comes in really handy when your school requires a super random style you couldn’t find an existing file for! (don’t worry – hopefully that will make more sense when we get there, you probably won’t need to know it, and it’s at the very end of the post so you can drop out before it and still get the most important info from the post)

I will probably never forget a conversation I had in one of my first grad school interviews – the professor interviewing me had asked me some variant of “why do you like science?” and I had responded by saying something about how I love how people from around the world could make these tiny contributions to the bigger puzzle and how other scientists can build upon them and you never know where the missing link will come from. How you might feel like you’re not making much of an impact at the time, but you seemingly small and inconsequential findings might prove to be just what someone needs to reach a point we call a breakthrough. 

His answer was basically that you should focus on trying to make breakthroughs and big leaps rather than being satisfied with small steps. 

5 years later and I still disagree with him… 

Go ahead and look behind the scenes of “breakthroughs” and you’ll see the work of countless other scientists. And if you want a look behind those scenes, turn to the “references” section at the ends of their papers! By references, I’m referring to all of those papers, books, websites, etc. that the authors got information from when they were researching and then want to give credit to when they use the information they got from them.  

In science articles, citations usually come up the most in the intro & discussion sections, where scientists talk about what was previously known (intro section), and how their work fits into what’s known (discussion). But note that when it comes to science there are waaaay more people who contributed inspiration and groundwork but don’t get cited explicitly because that would be basically impossible. Over the past few years, I’ve done a number of posts on biochemistry experiment “classics” that helped prove that genetic information holds heritable instructions for making proteins: the Chase-Hershey experiment; the Pauling & Ingram experiments; Griffith’s experiments, Avery, MacCleod, & McCarty’s experiments…

Imagine if you had to cite all those iconic biochemistry experiments every time you used a recombinant protein expression system (isolated the genetic instructions for a protein and stuck it into cells to make that protein on demand). The reference sections would be enormous! And they’re typically pretty huge as is!

This references section is sometimes referred to as a “Works Cited” section or a “Bibliography” (although those are slightly different – bibliography includes things you read and used as inspiration of sorts but didn’t explicitly cite in the text). It’s the end-of-the-work complement to in-line citations, which are where you give a brief nod to them at the place where you use their info in your work.

So, for example, say I published an article called “What does it mean to be a good scientist?” in 2021 in the journal Fake Journal of Fake Articles. And then I write a paper where I want to reference something I wrote in that article. I could do something like…

Aspects of being a good scientist include: working hard; recognizing that you are part of a much larger network of scientists; and, above all, being a good person (Bumbling Biochemist, 2021). 

The stuff in parentheses is an “in-line citation,” in this case, in the “Author, Date” Format. This is one format you’ll commonly see all though the formatting may vary. Pretending “Bumbling” is my first name and “Biochemist” is my last name, variations include:

last name only: (Biochemist, 2021) 

last name, first initial: (Biochemist, B, 2021)

etc. 

Usually, if there are 3 or more authors, you just write the first author’s name and then “et al.” in the in-line citations. And then, in the bibliography, you write them all out (unless there are more than ~10 (depending on the style guidelines) in which case you write the first ones and then “et al.”. Note that there’s no period after et but there is a period after “al” because it’s an abbreviation of alia. I still have trouble remembering this sometimes! 

Another thing I sometimes have trouble remembering is that the citations go inside of the sentence punctuation (e.g. before the period, not after!) I recently turned in a 10-ish page paper draft to my PI (lab head) who reminded me and then I had to go through 10-ish pages of sentences to fix them all!

When in-line citations are given in one of these unnumbered formats, the references in the reference section are often listed by in alphabetical order (by first author), although sometimes they’re listed in the order they appear.

Other citation styles just use numbers to refer to papers in the order they appear, so you’ll see things like

…being a good person (1). 

…being a good person [1]. 

…being a good person¹.

The next article cited would get a 2, etc. 

In this case, the reference list is in numerical order, so the papers are listed in the order they are cited (the first time – often papers are cited multiple times, but they just get the one number) 

There are pros and cons of author/year vs numbered. A good thing about author/year is that it lets you easily see whom the authors are referring to and how old the finding is (sometimes relevant). But a bad thing about it is that it breaks up the text – especially when citations are mid-sentence, it can be very hard to stay with the flow of a sentence when that sentence is stretched out over 10 lines and half of it is citations!

My favorite format is when citations are numbered, but I’m reading it on a computer and can hover over the number to get a pop-up window that tells me the work that’s being referred to. Some sites also have features where if you click on the number a side bar comes up with info about that work and links to visit it. But be ware, not all sites are like this so sometimes when you click on a link it will just take you to the entry in the reference section making you lose your spot in the text. Thankfully the backspace key and/or a little arrow should take you back to where you were! 

We may have personal formats we prefer, but usually that doesn’t matter because we’re not the ones getting to choose! Instead, we need to format things the way our schools or the journals we’re submitting things to want them! And there are >10,000 citation styles?! https://citationstyles.org/ I mean what the… why the heck are there so many? Were people just wanting to be unique? Or just cruel?

Unlike most of the browser-only tools which typically just have a few of the main ones (MLA, Harvard, Chicago, etc.), reference management tools usually have a lot of included styles to choose from, and there are even thousands more you can import. 

But, I’m working on writing my PhD thesis. And the school wants us to use a citation format that I couldn’t even find (it’s probably the same as one of the others but not worth searching manually through 10,000 to find…) – I ended up using custom-bib to write a .bst file to use in LaTeX https://ctan.org/pkg/custom-bib?lang=en It was a bit of a pain, but at least now I can get my citations automatically formatted the way I want (more on LaTeX bibliographies in a minute). 

Another difference between those web tools and true reference management software is that the reference managers often have integration with your word processing software. So, when I’m writing a paper I can go to the “references” tab to insert a reference, search my references for the one I want, and it will get cited in-line and placed in the bibliography section. 

I use Microsoft Word with a Mendeley plug-in, so I’m going to show you how that works, but I think it should be about the same for different software combos. Mendeley is free (for up to 2GB storage space which should be plenty to keep you going!) and you can download it here: https://www.mendeley.com/reference-management/mendeley-desktop 

When I mentioned searching for the reference I want, what I’m referring to (no pun intended here but now I’m trying to think of puns…) is that within Word I’m searching my Mendeley library. And within my Mendeley library is information about all the works I’ve ever thought that I might want to use in the future (either for citing or for re-reading). 

Most of the time, I import citations using a web importer browser extension: https://www.mendeley.com/reference-management/web-importer 

When you’re on an article page you just click on the Mendeley icon in your tool bar and import it. You also have the option to download a PDF of the article (if available) and you can choose to import it into a specific folder in your library if you want to keep things organized by subject, project, class, etc. 

You can access your library on the web or in the desktop version – and they all sync together (when you ask them to – so if you don’t see something you thought you imported, make sure you’ve synced!). 

In the libraries (web and desktop) you can also insert citations – it gives you the option to “Add manual entry” which sounds like it would be tedious and one of the things you’re trying to avoid by using the software! But, if you enter the DOI or the PubMed ID (PMID) or the ArXiV ID it will search for it and fill in the fields for you. (note: a DOI is a digital object identifier – basically a string of characters unique to that article, which you can find on the article’s web page for newer articles) 

You can also add citations from computer files. If you go to an article on the web there’s often a “cite this” button (or something similar) – when you click it it gives you options to export it to a variety of file formats optimized for various citation managers. Then you can import that file into your citation manager. 

One of the export options is often “export citation to BibTeX” – and Mendeley also has an option to export your library to a .bib file. Before a couple of days ago I had no clue what that was, but now I’m much too familiar with it (but still definitely not claiming to be an expert on it!)…

If you’ve been following along, you might remember that a few days ago I told you about a text formatting program called LaTeX (NOT pronounced like the balloon thing – instead the X is really a χ (Greek chi) – you pronounce it lay-tek or lah-tek or else people will get mad, or at least know you don’t really know what you’re talking about!). 

If you want to know a little more: http://bit.ly/latexlearning 

But basically it’s kinda like Word, except you write in “markup” which is code-y stuff and it generates a PDF. If you know what you’re doing (or at least fake it till you make it with the help of Google) it gives you more control over formatting things than Word does, which is great for text with a lot of figures. It’s waaaay better with handling math symbols & equations. And, my favorite part, it lets you easily reference figures, sections, etc. without you having to keep track of them (you can even use the \label{something} option to give your figures, etc, nicknames you can refer to them by in your markup text and it will stick in the Figure number, etc. and that number is updated if you decide to stick in another figure before it). I’ve been playing around with it a lot over the last few days and another cool thing I figured out how to do is use \newcommand{somethingtodo} to make shortcuts for long things I write out a lot as well as shortcuts to format things the way I want. 

I got ridiculously proud of myself the other day when I wrote my first new command – to reference something in bold and put parentheses around it. Then I got fancy and wrote one to write (Fig. X) where Fig. X is a hyperlink to the figure.  

\newcommand{\reffp}[1]{\hyperref[#1]{{$($Fig. \ref*{#1}}$)$}} 

Then, when I want to refer to the figure, I just type \reffp{figure_nickname} and it’ll do it!  

One of the powers of LaTeX is it’s REALLY good with inserting and tracking citations. You use a .bib file containing all the “metadata” for your citations (year, authors, etc.) and then a .bst file with the instructions for the style you want. There are some pre-included with packages like natbib, and there are also additional styles you can download. https://www.reed.edu/cis/help/LaTeX/bibtexstyles.html 

But I couldn’t find the one I needed. So I Googled and found a couple of blog posts talking about a software called custom-bib which lets you easily (though a bit tediously) make a custom .bst file with the format you want. You can download it here: https://ctan.org/pkg/custom-bib?lang=en 

then just open a terminal from the folder that you download it in (in Mac, if you’re in a Finder window you can right click on the folder and tell it to open a terminal window there). Then type latex makebst and then it will ask you a bunch of Qs and make the file for you

http://gabrielelanaro.github.io/blog/2014/12/01/latex-bibliography-in-5-minutes.html… & https://blopig.com/blog/2013/02/how-to-make-a-custom-latex-bibliography-style/…

Then you can use that file in LaTeX. If you’re using Overleaf, which is a browser-based program for writing & compiling LaTeX, there’s a new file option to drag and drop or select a file from your computer. If you’re using a “local” program that works on your desktop, I think you just tell it the file path before the name and/or stick it in the directory you’re running things in – but you probably know more than I do!

Then, in LaTeX, in the preamble, put

\bibliographystyle{yourbstfilename}

and then, in the place you want a bibliography, put 

\bibliography{yourbibfilename}

This bib file can be imported (such as after exporting your library as a .bib file in Mendeley) or, if you have the paid version (which I have through work) it has Mendeley integration so if your library changes, the .bib file in Overleaf will change too. 

For the in-line citations, I’m using the natbib package and, in the preamble, I’ve set it to make the citations like

(Paper1Lastname, year; Paper2Lastname, year)

\usepackage[semicolon,sort]{natbib}

\setcitestyle{authoryear,open={(},close={)}} 

note: the sort parameter tells it to sort the entries in the in-line citations in the order they appear in the reference list. I have my reference list sorted by author, so it’s sorting them by author here. I’m still trying to figure out how to get them to sort by date in-line, but alphabetically in the references… worst comes to worse, I can turn off sort and just enter them in date order – I checked and this won’t affect the bibliography itself. clearly I don’t know what I’m doing though!

Then, in the text, I can use 

\citep{} to have a citation with parentheses

and

\cite{} to have a citation without parentheses

there are also additional options, you can learn about here: https://guides.library.yale.edu/bibtex/bibtex-natbib 

Apparently .bst files work with the natbib package and depend on “bibtex” but there’s also a newer thing called “biblatex” which uses the biber or bibtex and I really have no clue what I’m talking about, but I found post on stack exchange by Alan Munn is so helpful! Here’s a snippet, and then the link to more

“bibtex and biber are external programs that process bibliography information and act (roughly) as the interface between your .bib file and your LaTeX document. 

natbib and biblatex are LaTeX packages that format citations and bibliographies; natbib works only with bibtex, while biblatex (at the moment) works with both bibtex and biber.” 

https://tex.stackexchange.com/questions/25701/bibtex-vs-biber-and-biblatex-vs-natbib

Speaking of StackExchange, the TeX – LaTeX Stack Exchange is a life-saver! If you have a question, chances are someone’s asked it! And hopefully someone’s answered it well – anyone can answer and then people vote the answers up or down. If you can’t find your question you can ask (but if you’re copying and pasting code, be sure it’s a “minimum working example” – no excess fluff or people will get annoyed based on what I’ve seen!)

Sorry that got super technical, but sometimes I think it helps to hear things explained by someone who knows just enough to get that thing done, as opposed to an expert who might talk way over your head and/or make you feel stupid. So if anyone’s in a similar boat, hope this helps. 

Oh and one more thing – these reference managers usually let you annotate and take notes on the PDFs if you download them. 

I found this helpful video by Fleur GL Helmink that compares 3 of the main reference managers: EndNote, Zotero, & Mendeley: https://youtu.be/nWlZ1rX9V7M 

Sorry this post was not well-organized (got exhausted) but hopefully it can help you get and stay organized! 

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0  ⠀ 

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