OHSU BioData Club: LaTex and Collaborative Writing Software Introduction

The slides for this workshop and their LaTeX source code were forked from this github repository under a permissive MIT license.

The aim of this session is to get you attuned to the basics of writing in LaTeX as quickly as possible. The material is presented as a set of examples. Broader concepts and techniques are explained as they arise. Each part includes exercises that can be completed on Overleaf, a free online LaTeX editor, so you don't have to worry about getting LaTeX and related tools installed on your computers.

We've yet to customize these slides for BioData Club, as they already do the job of introducing learners to LaTeX quite well. There is enough material in these slides for multiple workshops, but we'll at least aim to get through The Basics, and hopefully some of part 2 on Structured Documents. If you're already familiar with writing in LaTex, you should skip forward - also we'll have advanced users on hand to brainstorm and answer questions.

In our session, we'll access the the slides from here

Links to indvidual lesson files are below.

1. The Basics: ideas, syntax, equations, environments, packages

2. Structed Documents & More: titles, sections, cross-references, figures, tables, bibliographies.

3. Not Just Papers: Presentations & More: recap exercise, presentations with beamer, drawings with tikz.

Other useful links:

LaTeX project site

Glossary of Commands

Feel free to use however you like --- contributions welcome!

Further Slide Development...for down the road

You may need to install some extra LaTeX packages and system packages in order to build the slides yourself.

1. The minted package provides syntax highlighting. It is installed by default in recent versions of TeX Live.

2. The minted package calls out to the pygments syntax highlighter, which is written in python. The relevant package is python-pygments in Debian / Ubuntu (sudo apt-get install python-pygments).

3. There is a simple Makefile that manages the build. To use it, you'll probably need to be on Linux, and you will need make.

The slides include links to exercises that open in Overleaf. The exercise source files are hosted on github. If you want to use exercise files in another location, you can fork this github repository and then change the \fileuri macro in preamble.tex:

\newcommand{\fileuri}{https://raw.github.com/jdleesmiller/latex-course/master/en}

so that instead of pointing to jdleesmiller/latex-course, it points to your-github-user-name/latex-course. Then, once you've pushed your changed exercise files to github, the slides will load them up in Overleaf.

The deploy-to-gh-pages.sh script builds the slides using the Makefile and copies the slides over to the gh-pages branch, which is available at https://jdlm.info/latex-course thanks to github pages.

License

The slides and source are released under the MIT license. See the LICENSE file.

Original Credits

• Diana A -- found that exercise links had broken
• Sana A -- pointed out an error in part 1
• Andy Roberts -- the chick(en) image is from one of his articles
• Ruby Trinh -- for organising the original short courses