Integrating hands-on, experimental research into a zettelkasten
Hello all,
I'm a PhD student and an experimental material scientist, and I've used a zettelkasten via Obsidian for organising my review of the scientific literature. It's an incredibly useful framework for synthesising and summarising literature, but I remain unsure how to best integrate my original research (seeing as I'm yet to publish a paper!) Of course, in the humanities and social sciences the output of the zettelkasten consists of original research in and of itself, but aside from the review paper I hope to write I still have to get my hands dirty with electron microscopes and geochemical modelling software due to the nature of the field (not by itself a problem, as I love labwork).
But how I go from calculations in a spreadsheet or results from a machine to coherent zettels in obsidian isn't trivial. Does anyone have any advice about how to incorporate this kind of material into a zettelkasten?
Many thanks,
Patrick
Howdy, Stranger!
Comments
The data I collect in my programming work can sometimes find its way as observational notes in my Zettelkasten, but when talking about this with @Sascha who coached scientists over the years, a better idea could be to treat experimental data as external to the Zettelkasten -- as something to 'cite' and reference. 🤔
Author at Zettelkasten.de • https://christiantietze.de/
I also try to figure out how to make kind of academic workflow where bunch of things work together as a one living organism, system.
Literally an hour ago I downloaded Pandoc (to avoid manual formatting of the paper and focus more on the real research), prepared .bib file with all my references from Zotero and .scl file (prepared format of the paper of exact Scientific Journals) and added them to my note
And what happened: I wrote YML-text(with a path to .bib and .scl file) in the beginning of my note in Obsidian, Ctrl+P -> (Plugin) Insert a Markdown Citation -> (Name et., 2024) + Automatically written Reference in the end of the note -> If I am done with my paper -> Ctrl + P -> (Plugin) Enhancing Export to…-> docx file -> Paper is ready to upload.
Potential is - in the plugin I can add other necessary details, commands, even for preparation of graphs, maps and whatever I wish for my paper.
I want to check what else is available today after waking up in the morning.
To be honest, I did not write any kind of articles, papers, that is why I try to go with smart ways and make my workflow seamless and avoid minor, silly mistakes. Everything above I was figuring out with Gemini + a lot of errors with broken links, paths to folders and other typical, annoying things.
I am open to discuss all of it with you, let me know if you are in!
There are three activities in play, aren't there? You have to develop and perform the research, you have to consolidate the results, and you will have to write them up. Have you been using a scientific notebook, like Jupyter? That could be very helpful. Or you could consider making some or all the nodes in the Jupyter file into z-cards; of course, any nodes that execute code and display the results aren't going to be doing that from within the Zettelkasten so you would have to include references to those parts.
Z-cards might also be good for planning experiments and data analysis.
Once it is time to write up the results, you could work that up in the Zettelkasten and convert the results to the paper's format. The details would depend on what format the paper(s) need to be in, and what help the system can give you. Or you can plan and refine the structure and contents for the paper (or thesis, etc.) and use them as source material for writing the actual paper in some authoring system.
I recently wrote a conference paper entirely in my Zettelkasten. It wasn't an account of scientific research, though. It had to be in a simplified version of Docbook (an extensive XML language designed for publishing all kinds of written documents). I wrote a few scripts to do the bulk of the formatting and included inline XML for some of the more specialized bits like tables. It was a good experience because I had immediate access to my notes for the paper, which were in the form of z-cards. I did all this work in a provisional part of the ZK and now that it's done I've moved it all out of the ZK proper.