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# Writing and organizing literature notes for scientific writing
Vidianos Giannitsis (<mailto:vidianosgiannitsis@gmail.com>)
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Literature notes are a cornerstone of one's zettelkasten. Especially for scientific writing which needs to be based on bibliography, having notes on the literature you read is essential. Inspired by a chapter of "How to Take Smart Notes" by Sonke Ahrens - one of the best Zettelkasten books out there - which talks about the process of writing a scientific article, I crafted a heavily personalized workflow for writing and organizing my literature notes, which I wanted to present to you. Due to university, I have worked on assignments meant to simulate scientific articles and through them I refined this workflow to what it is today, which I am very happy with. I even wrote my own package for addressing part of this workflow, which will be a pivotal part of the talk. I have tried to not overcomplicate the talk, but a familiarity to zettelkasten and scientific writing is expected to get the most out of the talk.
This talk will focus on how Emacs has aided me in scientific writing and will cover how I use various packages for this. Featured will be: Org-noter, one of my favourite emacs packages which I use to annotate articles using org-mode while reading them. I will focus primarily on its integration with my org-roam-capture-templates and how it, org-roam-bibtex and ivy-bibtex work together to very easily create and flesh out literature notes for the articles I find, but I will also briefly mention how I annotate articles. Then, how I use org-roam to then take what I learned from this literature and create permanent notes on it which I can then add easily to my Zettelkasten. And finally, how I organize both literature and permanent notes on a subject using my own project, the zetteldesk package, and how I can very easily create a first draft of my work using this. With the draft created organically through my notes, it is then almost effortless to write the final work, as it consists simply of reading the draft, making small changes and fixes and perfecting it so it is a ready product.
## Links
- [Zotero](https://www.zotero.org/), the app I use for capturing
literature I find, which is unfortunately not in Emacs as I haven't
figured out a good way to do this from Emacs. (P.S. if you have a
good workflow for doing this from inside Emacs, I would love to have
a discussion with you because leaving Emacs annoys me).
- [Org-Roam](https://www.orgroam.com/), the bread and butter of almost
everything in my workflow. Org-roam creates my zettelkasten and is
the basis of the other packages here.
- [Ivy-bibtex](https://github.com/tmalsburg/helm-bibtex), the package
that allows Emacs to read .bib files and do things with them,
allowing for bibliography management in Emacs.
- [Org-roam-bibtex](https://github.com/org-roam/org-roam-bibtex).
Integration between the 2 packages listed above so I can easily add
literature notes to my Zettelkasten.
- [Org-noter](https://github.com/weirdNox/org-noter), the package that
does all the annotating. I can't take notes on an article without
org-noter, its just the best way to do it.
- [Zetteldesk](https://github.com/Vidianos-Giannitsis/zetteldesk.el)
my personal project which was inspired by making this workflow work
in Emacs. This package facilitates everything discussed in the last
part of the talk about organizing your literature.
## Bio
I am Vidianos Giannitsis, a 4th year chemical engineering student who loves to use Emacs. I have been using Emacs for about 2 and a half years and at this point it has become the most important part of my workflow. After seeing how awesome Emacs is, I was very inclined to learn elisp to truly customize Emacs to its limits. So I did, and at the start of 2022 I started working on a package of mine "zetteldesk.el". This package was inspired from "How to take smart notes" the well known zettelkasten book. I read something there and I was like, surely I can implement this in Emacs, can't I. And so I did.
I have watched EmacsConf for the last two years and I was interested in participating in it myself. Since I recently wrote a package of mine, I thought it was a good opportunity to make a talk of my own. So I made this talk about managing literature as it is something I believe I can deliver unique information and something I have worked on a lot recently.
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