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Choosing between Zettlr and Obsidian

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When I decided to start my digital garden , I had to look around for tools I felt confident using in the long run. After experimenting for some time, I narrowed down the list of requirements for the software I use to take notes:

  • Files are stored locally
  • In a format that guarantees long-term compatibility (such as markdown)
  • Interface is not in the way
  • Supports easy linking (such as wikilinks)
  • Does not force a structure on my notes (such as categories)
  • I do not need to include many figures, nor tables
  • But I do want Some support for equations
  • And I do want Some support for references
  • I don't need the program to render the notes in any format

The first few requirements are based on my workflow. I don't need to take notes on my phone and have them ready on my computer or the other way around. I always take notes when I am at my desk. The kind of note I would take on a phone is the kind of note I take on paper. I know this is not for everyone, but I am confident it is the same workflow for most people.

I have explored different programs, and none of them reached the level of either Zettlr or Obsidian . However, they are pretty different from each other, and that is what I want to discuss.

First, Zettlr is open source, and I believe in choosing technology based on their incentives . I have used parts of the code of Zettlr to understand how to parse markdown and render this website. Obsidian is not open source and probably will never be. Although it is free to use, it has some premium features. It is worth noting that in both cases, files are stored locally in markdown, and therefore there's no vendor lock-in, and if any of the programs goes out of business, I can easily port my project to another solution.

They both have a clean interface. Obsidian is more minimalistic than Zettlr. They both support quick links with the wikilink format. However, Zettlr offers a bit more configuration on how they look (adding text, referencing by title, etc.) Obsidian implements bidirectional links and a network graph to see how notes are linked to each other. It may sound like a minor feature, but it is great to quickly find orphan notes, put several together and understand our thoughts by proximity.

Up to this point, my favorite to use daily is Obsidian . I like the simple interface that does not get in the way. On the other hand, Zettlr falls in the category of authoring tools. It means it focuses on final products, such as a report, a paper, or even a book. You can export notes to different formats, handle bibliography and more. That means that a lot of the effort is put into rendering the notes correctly, while that is a feature I do not need.

Since I render the notes as a website with a custom script, I am interested in a tool that helps me author notes, find links, organize my thoughts. I find searching through notes easier on Obsidian. Writing overall has a lower barrier to writing thanks to the uncluttered interface. Zettlr calls itself a markdown editor , and that is not what I was after.

But , there is always a but. Zettlr is geared towards academic work. It means that it bundles some very nice features: for example, it renders equations written in LaTeX and handles bibliographic databases straight out of Zotero . Obsidian does not include these features, and probably it'll never do because their target customers are elsewhere. These two features are, in my opinion, killer additions to proper note-taking software.

In the end, I've reached a compromise: I take most notes using Obsidian because it feels quick and unintrusive. But if I need to take literature notes on papers that require more equations and proper handling of citations, I use Zettlr directly. After a while, I got used to referencing sources just by looking at the citation key in Zotero, and I use Zettlr even more sporadically, just for equation-heavy work.

I parse the notes for rendering as a website with a custom program, and I must confess that I barely look at it. I trust that the pages are looking OK or that someone will warn me if not. Splitting creation from publishing gave me a new influx of energy to start actively maintaining a website.

Other software I didn't like

Since some people keep asking and suggesting other programs, I must stop them right now: I don't intend to try programs just because they are there. There must be a stringent justification for me to spend time on them.

Many programs are not what I am after. For example, I am not looking for cloud solutions such as Roam or Notion. I don't trust either company to give them my notes. Secondly, I don't care about programs with bloated interfaces, such as Trillium and many others I've tried in the past. It is simply not my style, in the same way that Evernote is an awful choice for long-term storing of notes (look at their Linux support).

It does not mean that these same tools are not worth your time and money. Not all work in the same way, and, at least for me, the essential objective is to achieve low friction working. For me, this particular combination of tools works well. Perhaps in the future, there'll be other programs that can lower the friction even further.

Tags: #note-taking #software #obsidian #zettlr


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Aquiles Carattino
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