About
Biologists hardly ever use LaTeX. And I wonder why. With such excellent typesetting, everything you write in LaTeX looks beautiful. And it is absolutely free! Most biologists I know are so used to WYSIWYG (“what you see is what you get”) word processors like Microsoft Word and the ecosystem of everything that connects to them, that there is just too much inertia to try to learn and incorporate LaTeX in their workflow. Additionally, I find myself stuck with using MS Word often because my coworkers or collaborators do not use LaTeX. So I decided to write this primer as an introduction to LaTeX. I myself am no expert at it, was introduced to LaTeX only towards the end of my PhD (but was instantly convinced by its beauty to write my dissertation using it), and have only really used an online editor. Hence, my primer is in no way exhaustive or complete, but it is a start.
Background
LaTeX is a document preparation and typesetting system. It was initially developed by Leslie Lamport. LaTeX uses standardized tagging conventions to define the structure and style of the document and combines it with the typesetting system of TeX to generate an output file (usually a pdf). TeX itself was the masterwork of Don Knuth. In plain terms, you do not have to worry about formatting as you write the text- LaTeX provides you the ability to generate a document that looks really professional with minimal effort.
Getting started
To start using LaTeX, you can download and install a LaTeX editor and compiler, or you can use an online LaTeX editor like Overleaf (there are many such online editors out there) to get started right away. The latter also gives you the option of sharing and collaborating with others, which can be very useful!
Let’s say you have a document in mind you want to compose in LaTeX. The first and easiest thing to do is to look for a template for that document type. There are so many resources out there, and people are often generous with openly sharing their templates. The online editors also provide many templates that you could use. But be prepared, you will come across issues that aren’t straightforward (say wraping text around a figure or using biology specific symbols for genotypes or an easy way to write labnotes which involve inserting tables and text and figures all on the same page), but like with all things open source, you may go down a rabbit-hole, but if you put enough time into it, you’ll figure out a way past the issue (or just ask someone who uses it all the time!). Understanding the basic structure of LaTeX documents is useful at this point.
The accessories and resources
Manuscript templates: Most biology journals now do accept LaTeX formats and provide their own templates for writing the manuscripts. See the PLoS Biology template, for example. You can find many templates on Overleaf as well.
Bibliography manager: BibTeX. I use BibDesk and Skim to store, cross-reference and annotate my pdfs of journal articles as well as manage my citations.
Lab notebook templates: I find this notebook template by Jeremiah Faith particularly useful to meet the challenges of the nomenclature I need to incorporate in my own notes.