Emacs and knowledge management for scientists

• scimax

  19 1,000 6.1 Emacs Lisp

  An emacs starterkit for scientists and engineers

Maybe give scimax a go?

• Joplin

  771 43,584 9.9 TypeScript

  Joplin - the secure note taking and to-do app with synchronisation capabilities for Windows, macOS, Linux, Android and iOS.

As much as I love and eat and breathe emacs, you might want to check out different tools. Like org-mode and friends, this does not help you produce pdf reports (except maybe via cut-and-paste), but you might want to check out Joplin, which is vaguely like a free, open-source version of Evernote. Notes in Joplin are written in markdown, equations are handled via KaTeX notation, and chemical equations are handled in mhchem. See Joplin’s markdown guide.

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• org-roam-bibtex

  10 560 3.1 Emacs Lisp

  Org Roam integration with bibliography management software

  

In addition to org-roam, I would recommend checking out https://github.com/org-roam/org-roam-bibtex for attaching notes to specific papers that are indexed by an application like Zotero. Some good tutorials for it are here: https://rgoswami.me/posts/org-note-workflow/ and https://blog.jethro.dev/posts/how_to_take_smart_notes_org/ and https://emacsconf.org/2020/talks/17/ . Since current org-roam (post-v2) uses the normal org-mode "id" form, you can make any "headline" into an roam-registered node. You could then split your long derivations into different headlines, where the body of the headline or descriptive text could refer to prior nodes, but any latex is inserted using org latex blocks https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html . You've maybe already considered this (and I wouldn't be surprised if local references were easier to do in straight latex), but org-roam-bibtex is really nice for interfacing with your citation system for other papers.

• citar

  33 464 5.6 Emacs Lisp

  Emacs package to quickly find and act on bibliographic references, and edit org, markdown, and latex academic documents.

  

The citar package, which I created, has note integration packages available for both org-roam and denote (along with zk).

• zk

  10 115 7.1 Emacs Lisp

  Emacs packages for working with Zettelkasten-style linked notes (by localauthor)

The citar package, which I created, has note integration packages available for both org-roam and denote (along with zk).

• Dotfiles

  4 27 4.1 Emacs Lisp

  Just a repository for my dotfiles (by AuroraDragoon)

For describing my workflow very briefly (not as well as Sonke Ahrens in the aforementioned book, but I will try), I try to follow the main points of Zettelkasten. Whenever you learn something, take notes about it. Make the notes brief, but very descriptive. Give it a large title describing everything contained in it so you can find it easier later. If its too large, split it into multiple files, so the note is atomic (meaning it can no longer be separated into multiple files). If you don't have time to write a note correctly, make a fleeting note about it to remind you and write it later. Densely link your notes with one another. Thinking about the connections between notes is sometimes half the work of writing it. This way, I never lose information. If I need something later down the line, I can always search with org-roam-node-find, as I use very descriptive titles as I mentioned. If not, there is also grep, which if you are not aware is a text editing utility that allows for searching all your notes. There are many grep tools in Emacs (i.e. counsel-rg being the one I use personally). For more explanation, you can check my literate org-mode config.

• zetteldesk.el

  10 111 3.8 Emacs Lisp

  Zetteldesk.el is an emacs library built on top of org-roam with the purpose of easier revision on various subjects and a better outliner tool for emacs

For publishing stuff, Emacs has a very rich ecosystem. Org-export libraries are very powerful and allow you to export to virtually any format you desire. There is also org-publish for publishing your work, which works very well. However, when you have a bunch of org-roam nodes, it is not so easy to export all of them. I have personally created a tool for gathering a lot of your org-roam nodes in one file, your so-called "desktop" which can be used for revision of topics, writing manuscripts for articles or just straight up publishing your notes. You can find it here.

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

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