I would never claim to have the ‘optimal’ research workflow. However I always find it interesting to see the different ways in which we optimise our working day (and find the little things that bring us joy). This is a high-level overview of my typical research workflow as of 2024
Writing
- I avoid using Word as my writing environment at all costs and rather make use of a pandoc-assisted workflow. Which allows me to write in a distraction-free, plain-text world and use the relevant templates to generate files that conform to journal requirements. This allows me to focus on the content and not get distracted by the minutia of formatting.
- I primarily use Quarto to facilitate this process, with the Quarto manuscript project type being my go to for writing-specific projects.
- I also host all of my writing projects as individual repositories on Github, where I will also host the (in-progress) writing on GitHub pages. This allows for easy sharing between collaborators and allows them to access different filetypes of the document
- Comments/feedback is done through pull requests - which allows us to compare changes before accepting them, and keeps a record of changes
- It is also possible to have an hypothesis.is overlay on the actual webpage - allowing collaborators to make ‘word-style’ comments there as well
- The additional advantage of using the Quarto ecosystem is that it allows you to embed code chunks within the file or as additional notebooks
- This allows you to integrate analyses with writing and create ‘living documents’. Ensuring that up-to-date results are always shown and is not reliant on someone manually replacing/updating them.
- I use Zotero as my reference manager, which has the added benefit of integrating with Quarto allowing you to import bibliographic entries while writing.
- I still prefer to use individual folders in Zotero for each project and dropping relevant references into them, which I can then have automatically expert as a
.bibfile to the relevant project file as opposed to the Quarto reference workflow but for very collaborative projects where many people are expected to write and add their own citations the the Quarto backend is better. - I use the Better BibTeX plugin to generate (what I find to be) informative citation keys for each reference
- I still prefer to use individual folders in Zotero for each project and dropping relevant references into them, which I can then have automatically expert as a
- I am still a devout pen and paper user when it comes to generating and processing of ideas and concepts and use a dated diary as a way to temporally segregate my notes.
Science and research
Development
- In the interest of full reproducibility and transparency, I post almost everything I write (see above) or develop on GitHub.
- I use a mixture of
JuliaandRfor any statistical computing or modelling exercises. (I would not say that I have strong opinions but lean in favour of Julia for doing development but often still turn to R for data wrangling - something I find well suited to with the tidyverse ecosystem) - I primarily use Visual Studio Code for everything I do (writing and coding).
- I adore the
fairyflosstheme, and always have avscode-petroaming around my workspace.
- I adore the
- For dedicated R users I can see an argument for RStudio though.
Graphic design
- For data-driven figures and plotting I am a devout
ggplotuser, although I am trying to embrace theMakieecosystem in Julia… - I use a combination of Fresco and Illustrator CC to make non-data-driven figures and diagrams.
- Using Freso to create the smaller ‘assets’ and Illustrator for overall design, layout, and text.
- I use Adobe Color to generate colour palettes, both from the colour wheel as well as extracting them from figures.
- I use the Color Oracle plug-in to aid in designing figures that are accessible for colour impaired audiences.
- Despite my dislike for Word and Excel, I must admit to using PowerPoint for all my presentations - although the temptation to play with Quarto presentations is strong…
Hardware and Software
- I am a dedicated MacOS user, having not been brave enough to dip my toes into Linux.
- I am currently using a 2024 M3 14” MacBook Pro with 48 GB of memory and a 3rd generation 11” iPad Pro.
- I am currently using the Hobonichi A5 Hon as my ‘old man paper calendar’ writing tool (few things will beat the Tomoe River paper writing experience).
- For pens I range between Sailor, Platinum, LAMY, and TWSBI, and have recently fallen in love with Wearinguel and Colorverse inks.
Miscellaneous
- I am not a fan of productivity apps (I spend more time fiddling than using) but do use WakaTime as way to see see which projects are getting the bulk of my attention.