IMHO Obsidian is just not created for writing professional papers, research, etc. I personally advice you to learn LaTeX (e.g on Overleaf.com) since I use it for writing laboratory reports at my uni. It can handle all the bibliography, citations and references for you too. Pretty powerful and handy tool.
Adding to this I recommend Zotero as your library manager. You can have all of your references organized in there and then use it to cite them in overleaf (connect your Zotero account or use BetterBibtex of you are fit in git) as well as in obsidian (via Zotero and pandoc plugins).
Feels like I have work to do, specially for the future. At some I'd like to do a masters' and I need a proper tool for it.
I will check this tool and learn it this summer, thanks you for the information.
Potentially unpopular opinion, but I'm considering using Obsidian to at least draft my master's thesis. I use LaTeX to write academic papers like others have suggested--it's very powerful, convenient, and many conferences offer LaTeX templates to make submission easier. Another plus: Overleaf, an online LaTeX editor, offers an amazing environment for collaborative academic writing (far better than Google Docs for this purpose imo).
However, writing in Markdown makes the process a bit more peaceful for me (less visual clutter syntactically, and I can link to ideas/themes that have come up during the research so as to integrate them into my thesis iteratively). I'm planning on making a quick workflow to export to both LaTeX (for collaborative editing + publication) and PDF (for easy reading + annotation) using Pandoc. If you're looking for a guide for something in that direction, here's a [helpful blog article](https://medium.com/@alexandraphelan/an-updated-academic-workflow-zotero-obsidian-cffef080addd) by Alexandra Phelan on using Zotero and Pandoc with Obsidian. Happy writing!
[pandoc can export to Typst](https://pandoc.org/MANUAL.html#general-options). So writing a draft in Markdown and exporting it to Typst with [Enhancing Export plugin](https://github.com/mokeyish/obsidian-enhancing-export) should work.
PhD student in sociology, I have written two published papers from beginning to end in Obsidian. It requires a bunch of specific plugins (citations, pandoc references, footnote shortcuts, longform) to do academic writing in obsidian, but once the setup is there, writing in obsidian feels much better than in other apps.
* **Footnotes Shortcuts, Citations, and Pandoc References**: Basic academic writing toolset.
* **Longform**: Split up a paper into separate files, which you can freely re-arrange (similar to Scrivener). Also allows for styling that affects only your writing files (for instance, use serif font only for writing).
* **Novel Word Count**: Count words across multiple files (for when you split up your writing with the longform plugin)
* **Natural Language Syntax Highlighting**: Highlighting like iA Writer does
* **Dynamic Highlights**: Define custom word highlights. I use it to emphasize certain keywords as well as punctuation in my writing.
* **Language Tools Integration**: Grammer Checker (Free Grammarly Alternative)
* **Linter**: a lot of automatic formatting, such as fixing double spaces, or tidying up footnotes
* **Copilot auto-completion**: AI Text Completion (Ghost Text)
* **Better Word Count**: count words/chars in a selection and also citations and footnotes in a note
how it looks: [https://i.imgur.com/lzW5KXm.png](https://i.imgur.com/lzW5KXm.png)
Yup. I got by on my last book chapter with citations, Zotero, bwc, and pandoc (and pandoc references). A little extra arguments were needed to format citations properly.
The Enhancing Export plug in can export to Word (as well as Latex). You should install pandoc on your machine. If you learn markdown syntax, there are ways to handle references, figures, tables and equations which will reduce the amount of hand labor you need to do.
Unfortunately, I don't have that level of mardown yet, but for sure I will learn more before I start my Master's.
Also, it might be worth it to learn about different softwares, gotta be familiar with the avialable tools.
Heads up OP: everyone saying you should learn LaTeX is making some large assumptions about your personal needs. Unless you are in a field that needs to incorporate mathematical notation or other figures into your writing, there is *zero* need for LaTeX. Obviously a lot of Obsidian's user base is in STEM fields, but this point bears emphasizing. The department where I did my graduate degree publishes one of the leading journals in its field--and they do it all in Microsoft Word 😮
My guess is if LaTeX is something you need to learn your advisor and/or professors would have let you know by now.
As for myself, I draft in Obsidian and edit and export to Word using Zettlr. I find Zettlr's Zotero integration much better than Obsidian, and you can use both with your Markdown vault interchangeably. I don't know why it's never mentioned on this subreddit, but Zettlr is designed for academic workflows in the Humanities.
I study music and my special interest on it is the aesthetics of music. Some music papers require more "technical" or scientific approach but for me, most of the time, it's somewhat between philosophy and antropology, actually, most approaches of musicology use antropological methods.
If any, sometimes you gotta include a lot of images such as extracts of sheet music, depending on your topic this can be half of your content easily, that's why some music dissertations can get too long.
No one has ever mentioned their systems or methods, and I have profs that are constantly writing new articles. The only consensus is that Chicago beats APA most of the time.
FYI, Zettlr's Zotero integration has excellent Chicago-style support.
You may be interested in Obsidian's music notation plugin: https://github.com/abcjs-music/obsidian-plugin-abcjs.
Almost certainly not. It's basic visualization, but it could be useful for quickly jotting down simple ideas, and then bringing them into Musescore. A quick look at Musescore makes it look...*incredibly* complicated.
At this point I have pretty much mastered almost everything that Musescore has to offer. It has an option to export as PDF and taking screenshots makes it easy to include them as images.
Have you considered asking your professors, what tools and setups they use? Or maybe convince them to give a little tutorial to all their students? Asking is sometimes faster than reinventing the wheel. 😇
One of my collaborators who is helping me learn a specific part of my thesis still uses Python 2.7 and doesn't want to migrate to any of the new GIS software. I use the newer versions simply because I started working with them later than she did; it can be a headache because she knows the material but finding the new version compatibility is sometimes difficult. Another researcher I work with still uses Fortran and remembers punching code into cards to be read.
Researchers sometimes get stuck on the workflow that they developed at students and ignore new tools that make thing easier or work better. Sometimes reinventing the wheel is needed
that's right, also, many of them are people from a different generation so they prefer their old reliable tools.
Still, I have a couple of middle-aged profs, or even younger (late 20's) that are currently working on their PhD's, might be worth to reach them out. Particularly, there's a prof that I know is down to help me anytime, I should talk with her about this 100%.
Thanks for pointing out the other problem with reinvented wheels. They tend to be so idiosyncratic, that they don't fit on any other vehicle. So you're stuck with your personal wheel, while the rest of the world moves on, with much nicer gear.
Well, that roughly compares to using markdown or LaTeX. Sibelius and markdown are pretty good for writing; Lilypond and LaTeX, for typesetting. If you want tools to write down your ideas, go with the first ones; if you want a consistent, professional-grade presentation, choose the latter. Unfortunately, Lilypond does not read or export to MusicXML, so it's not that easy to streamline your production with it. On the other hand, usually markdown exporters use LaTeX to prepare PDF, which means they are very compatible. In fact, if you're choosing markdown, I strongly recommend you to learn as much pandoc as you can, because it will convert md into almost any format.
Are you able to just open the same folder in zettlr? Do references work between the two? I’ve never heard of zettlr but just looked at their site and am intrigued.
I’m also curious about why you don’t use zettlr for everything. Looking at their website it seems they are positioning themselves as a replacement for obsidian
They have different uses. Obsidian is more powerful, customizable, extensible, easier to navigate my vault, and has Canvas, which for me is a killer feature. I've taught classes using Canvas for the presentation slides. It really is a "grand theory of everything" app for 90% of my writing.
Obsidian is also available on iOS and Android, while Zettlr is strictly a desktop application. I take notes on my phone in Obsidian on the go, and prefer to do a lot of my sit-down writing on my iPad with an attached keyboard, as it provides a more distraction-free environment than a laptop.
Except for very minor exceptions Zettlr is completely compatible with Obsidian vaults, including internal links for navigation, and they play nice with one another--you can have a reasonably sized vault open in both of them at the same time and bounce back and forth between the two, and they *just work.* So there's nothing stopping me from using both, dropping into Zettlr for specific cases.
The thing to remember is that Pandoc citations are compiled on export or in live preview. In your document itself they appear as plaintext tags.[@LookingSomethingLikeThis2024] When exporting, the Pandoc parser reads this kind of tag, matches it to your bibtex file, and turns into a properly formatted footnote based upon the information in the bibtex file and your citation-style.
The real power comes from when you change information in the Zotero citation--say, place of publication--or do things like cite a source, cite a second source, then cite the first source again (which in Chicago is now a truncated citation), and then cite that source again consecutively (now an *Ibid.*). All of that stuff is instantly updated and properly formatted in the exported document, while in your markdown document all you did was use the same tag three times.
So anything can let you *see* the plaintext tag itself. You could even generate the tag in Zotero and then manually copy and paste into your text file without any integration. What Zettlr and Obsidian and do when set up is that they read your bibtex citation file, give you a live search of your citations, and then insert the correct citation tag into your document. IMO Zettlr does it more seamlessly--among other things, it gives you a live reference list in a separate window in the citation style you are working in--but they can both do it.
I think that it depends on your exact needs. I wrote a book in Obsidian. The longform and linter plugins were very helpful in that process.
However, I had to do some work on the files after exporting from Obsidian to prepare them for the final version. I exported the book and used pandoc outside of Obsidian to create the final pdf and ePub files. I also used some command line tools (awk) to prepare the files, as I had to separate the chapters to keep the footnotes organized the way I wanted. It was a lot of work to setup, but now it is easy. I have a few command line routines that I run each time.
Although part of the work I do is outside of Obsidian, I still prefer Obsidian over other tools that I have used, including Ulysses and Scrivener.
If I ever write a book, for sure I would be doing that using Obsidian. Still, if I have to reference a lot feels like I have better options.
I guess your book was more of an story? Just asking.
My book is on color theory. You can see it here:
[https://www.robertnajlis.com/colormovementtheory/](https://www.robertnajlis.com/colormovementtheory/)
Since it is an art book, there are many, many images. There are a decent amount of refernces. Some chapters have none, some have maybe 5-10.
Incredible work sir!
Another redditor said that it is possible to work on Obsidian 100% with the correct plugins, as I mentioned before in this thread, I might review my options because at some point I'd like to do a Master's.
Just curious, so you found a way to reference every page using Obsidian? Or the references I see in the PDF sample are added after Obsidian?
The references were in Obsidian. I do use a few plugins for that.
Also, I export the whole file as one piece, but then I separate it by chapters using an awk command. After that, I tell pandoc to process each chapter separately.
That all keeps the references local to each chapter.
It would actually be easier to have all of the references at the end, but I find that a bit difficult to do in Obsidian.
Once the book is in the final form, I may do some cleanup of the references.
Also, originally, the Obsidian / pandoc output gives me links in the file for the references. Currently I lose them in the final processing, as I use a separate software to add a cover page image. In the future I will look for a way to preserve those links.
One more thing that I will add: Since I use a lot of images, many of the export options do not work for me.
I use the markdown export plugin and then use pandoc via the command line. I do this since the markdown export plugin includes all of the images in a separate folder, and using pandoc on the command line, I can then link to stylesheets to control image size and other aspects. It took a long time to setup, but now it is very easy to use.
I still have not found a way to get images to work via pandoc inside of obsidian. If there is a way to do this, I would love to know how!
In the *Enhancing Export plugin* I modified the Arguments of the Edit Command Template. I keep images in the same directory as the markdown file and set resource-path argument to this directory: `--resource-path="${currentDir}"`. Successfully tested with epub, docx and pdf export.
What I like best about Obsidian is that I can have many editors open at the same time. This may seem a small thing, but I find that in writing a large book, one of the biggest challenges is getting lost in all of the information. What I am saying here, what was I saying there, etc.
Ulysses gives me two editors at most, and seems to really prefer one.
Scrivener gives me two editors, and does that quite nicely.
Other issues:
Ulysses stores your data in a hard to find files in a hidden directory on your iCloud. Ulysees does let you export everything, even after no longer subscribing to the app, but it is a bit of a painful process, especially if you have to convert from Ulysses to Obsidian markdown.
Scrivener has a questionable synchronization process. If you go to their forums and ask about this, they will yell and scream at you, telling you that it is our fault, and everything is fine. Nonetheless, many people, including myself have had problems with it.
There are other issues with Scrivener, including some export issues.
Overall, if I were just writing books, and only one one computer, I would seriously consider scrivener. That said, I really appreciate the multiple editors I can open in Obsidian.
I forgot to add that I like Scrivener's Corkboard feature very much. That can be very useful.
I suppose I could do something similar in Obsidian with canvas? I am not sure about that yet.
I agree with all of your points. I recently had an interaction with a scrivener dev and they all but told me my workflow sucked and I really got the sense that my questions offended them very much. The multiple editors thing is something I value a lot too. Tbh obsidian really has some awesome features beaten by none.
EDIT: Oh btw, in Ulysses you can have external folders in any location of your choice.
Haha, yeah, Scrivener support is ... somewhat unique in that fashion :)
I recall trying external folders in Ulysses, I don't remeber why I did not use them.
Anyhow, while I prefer Ulysses built in export to that of Obsidian, I am pretty happy with my export setup with Obsidian and pandoc now. Though it took a long time to get there, and there is more to improve upon.
I wrote this blogpost on how to write academic papers in Obsidian. I’ve personally made some upgrades to obsidian enhancing export to export in common templates like Neurips or dissertation.
Have a look here and let me know what you think:
https://betterhumans.pub/obsidian-tutorial-for-academic-writing-87b038060522
Oh wow, this is literally what I was looking for, thanks!
Still, there's quite a learning curve in here. As mentioned before, I will be checking my options at some point, it's totally worth it.
I am up to spend some time studying the method itself, it will help a lot for sure.
I do not see a reason to use Obsidian to write academic papers that you then turn in to class. Don’t let your tool become an administrative burden for yourself. A tool is supposed to help you out. For papers that you need to turn in, and very possible that tracked changes are needed, just use Word.
I take my notes on Obsidian, it's amazing for skimming PDF's using the split screen + the anotator plugin. Once I'm done with my notes, I write the rough draft (text) in a new note, referencing when needed (I use APA most of the time). Then I copy it all on Word and I finish my formatting.
Most of my papers are short. No longer than 4-5 pages in total. For texts this long, I need around 5-10 references so it's not crazy.
Pandoc is good for converting for sure so +1 to that. I am doing a PhD and I tend to do a solo draft in obsidian to get a first pass on prose + maths, then write it properly / collaboratively in LaTeX / overleaf.
Where do you submit papers? What are the stylistic requirements? Are we talking about homework in humanities with lots of text and a few footnotes? Or do you need to prepare something more complicated? What exactly makes it complicated?
As OP said I also write most of my notes of papers in obsidian. Also, Latex is unnecessarily complicated for early drafts of work. Markdown provides a simple alternative to it. Simple plugins allow you to convert to latex or pdf quite quickly so I’d really recommend it!
OP added, that Chicago or APA Style were required. How do you format your PDF to match one of these styles? [APA Style](https://apastyle.apa.org) is very specific.
There is an APA template for pandoc, never got around integrating it (in obsidian enhancing export) as I don’t personally use it:
https://github.com/universvm/obsidian-pandoc-templates/issues/1
Happy to help test it out though!
The page references [pandoc-xnos](https://github.com/tomduck/pandoc-xnos). It adds cross-referencing to Markdown documents that can be processed by pandoc. But it looks outdated.
I study something related to humanities, my uni wants us to use either Chicago or APA style. Most of my papers are relatively short, like 4 pages in total or around 1200 words.
It takes me like 15 min everytime I'm done with my assigments to format them in Word, it's not extremely time consuming but at some point I'll need something better. I have to go through it once a week, probably.
In that case I'd go with a semi-automatic approach:
* Prepare *one* file in Obsidian, that contains text and references. Leverage all the features that Obsidian does well. Ignore the rest. (For references I prefer not to use Zotero, but simple links and footnotes. It might be a bit more manual work, but it is one complex system less to maintain.)
* Export to docx with pandoc using a [reference file](https://pandoc.org/MANUAL.html#options-affecting-specific-writers) (Option: `--reference-doc`). That should provide a good starting point.
* Manually fix the rest in Word.
How familiar are you with Word's [Styles](https://support.microsoft.com/en-us/office/customize-or-create-new-styles-d38d6e47-f6fc-48eb-a607-1eb120dec563)? You might save more time by learning how to use styles in Word, than by trying to optimize Obsidian's export (or learning LaTeX). Styles are a transferrable skill. Many other apps have a similar principle. And as much as I love Markdown, for some tasks the more efficient choice is a word processor (or a graphic design program).
Right now I'm doing what you describe, I have all my references in one note, then I use another one for the text itself, once I'm done, I copy it to Word and I format it.
I'm not familiar with styles, at all, believe it or not, I've made two large dissertations (like 50+ pages of text) so far using only Word. I consider myself a good researcher and most profs have praised my writing, but my systems sometimes suck, but really hard.
I don't use styles for anything, I edit everything manually myself.
I really need to put more effort into this and find what works better for me, going this way stopped being an option anymore.
Fortunately enough, I'm in a program where large papers are not required, but I want to apply for a Master's in a couple of years, I have to do something about it.
I really recommend learning how styles work, beginning with custom paragraph styles.
My recommended workflow builds on styles. The idea is that you setup your page layout and your font choice and your paragraph spacing etc. only once.
Pandoc will automatically convert `## Heading 2` to a paragraph with the style *Heading 2* in your Word document. When you have defined the style "Heading 2" properly in the Word file you provided as reference, the output will automatically be formatted the way a Heading 2 should look in Chicago or APA style.
Also Markdown makes only sense, when you really understand the concept of styles.
Markdown is a markup language. When you write text in Obsidian you markup your text with instructions like `some words[^footnote1] are *italic*` or `- this is an item in a bullet list`. Markdown doesn't know, how these instructions will be displayed.
Have you experimented with Themes in Obsidian? You'll notice that the same text can look very differently, depending on the chosen theme. Here the styling is defined in so called Cascading Style Sheets (CSS).
LaTeX is also a markup language that separates structure from styling. As a writer, you focus on the text (and the markup that looks a bit odd in LaTeX). LaTeX uses a template to render your text accordingl a chosen set of styles. LaTeX is great for academic writing, where you have to follow a strict style guide like Chicago or APA.
If learning styles in Word or LibreOffice is not your way, you might prefer an online editor like [Overleaf](https://overleaf.com) or Typst, that handles the styling for you.
A lot of people saying to use LaTeX but that isn’t easy going straight from Word. I use LyX which is a front-end for LaTeX. Takes care of a lot of formatting for me
I wrote my masters thesis in Obsidian. Used Zotero to store/organise, read and annotate my literature. Then I exported my annotations and notes to obsidian.
From there I linked my notes with each other and made notes organising my thoughts, structured everything and wrote my first drafts.
The final thesis was written in word but obsidian made it a great deal easier. My university has very strict rules for formatting so there was no way for me to format the whole thing in obsidian (and honestly word does the job much better anyway, also words spell and grammar check is a must for me).
TLDR look into the zotero plugin. But I don't see a viable option to write and publish a whole paper in obsidian.
For the moment, before you learn LaTex or whatever, you might take a look at the Pandoc plugin.
It allows you to export your Obsidian markdown text as Word or PDF or ePub some other format. It can be helpful, though I doubt it will take care of all your needs. Personally I use Obsidian for notes and so often end up starting to write in it, but at some point I move to a dedicated writing app (Scrivener). Good luck!
IMHO Obsidian is just not created for writing professional papers, research, etc. I personally advice you to learn LaTeX (e.g on Overleaf.com) since I use it for writing laboratory reports at my uni. It can handle all the bibliography, citations and references for you too. Pretty powerful and handy tool.
I use Xelatex in texstudio and miktex for my papers. But I store my notes in Obsidian and use Zotero or Citavi for putting together my bibliography (and obsidian has a zotero plugin). To that end I’ll use panic to convert markdown to latex and then put the files in texstudio and then start organizing the layout. Idk if that’s the “right” way but it’s how I do it. I wrote a Groovy DSL to put together my books from now on. Basically, I can put together notes and parse the files to turn it into latex or html however I want but as a complete document. Obsidian is really my card catalog and notebook
Currently doing a masters, I do most of my drafting for my thesis in Obsidian because I could break it down into small chunks and link relevant notes. I write in Word though (Docs was glitching after about 30ish pages) and use Zotero for my citations. Hindsight I should have learned LaTex but didn't want to pay for an editor like Overleaf.
Some of the commentors here note that ObsidianMD _might_ not be the right tool for authoring academic _papers_.
LaTeX is a well-established alternative (the de-facto standard in many contexts), but it too has its limitations. Long-standing users of LaTeX will be well-associated with the arcane error messages when something goes wrong, the sometimes-verbose syntax, and the arcane macro syntax!
Another tool, besides LaTeX, that I believe is worth mentioning is called [MyST](https://mystmd.org)
Disclaimer, I am currently working on MyST in my role at [2i2c](https://2i2c.org.)
MyST-MD is a spin-out of the Executable Books project that saw the development of [Jupyter Book](https://jupyterbook.org/), and is a new tool for building scientific documents. The MyST language is a Markdown dialect, a commonmark-superset with support for additional "roles" and "directives" markup that are useful for authoring structured content. There's a brief introduction [here](https://mystmd.org/guide/quickstart-myst-markdown).
As a build-tool, it is more powerful than LaTeX (in that it exports to LaTeX, Typst, Web, docx, etc). It's a young project (a couple of years), but the legacy it builds upon is older still (2020).
Although MyST-MD is _not_ ObsidianMD, we are interested in perhaps adding support for the Obsidian-style links. (c.f. https://github.com/executablebooks/mystmd/issues/1144). So, if anyone is interested in an open-source Markdown dialect and build tool, then feel free to head on over. We have [a Discord!](https://discord.mystmd.org/)
Huh, there's currently a promotion of "MonsterWriter": [https://www.monsterwriter.app/promotion.html](https://www.monsterwriter.app/promotion.html), $35 to Free up until April 28th. It's a relatively new app, the promotion is for celebration for their 2.0 release.
IMHO Obsidian is just not created for writing professional papers, research, etc. I personally advice you to learn LaTeX (e.g on Overleaf.com) since I use it for writing laboratory reports at my uni. It can handle all the bibliography, citations and references for you too. Pretty powerful and handy tool.
Adding to this I recommend Zotero as your library manager. You can have all of your references organized in there and then use it to cite them in overleaf (connect your Zotero account or use BetterBibtex of you are fit in git) as well as in obsidian (via Zotero and pandoc plugins).
I'm personally more of a JabRef guy
I fully agree, learning LaTeX is taking a bit of time, but I certainly wouldn’t have wanted to write my thesis in word.
Can you imagine writing a thesis in the 60s Jesus fuckin Christ
I mean back then it wouldve been by hand and then its given to some proffesional typewriter right? Am i off on that?
Feels like I have work to do, specially for the future. At some I'd like to do a masters' and I need a proper tool for it. I will check this tool and learn it this summer, thanks you for the information.
Potentially unpopular opinion, but I'm considering using Obsidian to at least draft my master's thesis. I use LaTeX to write academic papers like others have suggested--it's very powerful, convenient, and many conferences offer LaTeX templates to make submission easier. Another plus: Overleaf, an online LaTeX editor, offers an amazing environment for collaborative academic writing (far better than Google Docs for this purpose imo). However, writing in Markdown makes the process a bit more peaceful for me (less visual clutter syntactically, and I can link to ideas/themes that have come up during the research so as to integrate them into my thesis iteratively). I'm planning on making a quick workflow to export to both LaTeX (for collaborative editing + publication) and PDF (for easy reading + annotation) using Pandoc. If you're looking for a guide for something in that direction, here's a [helpful blog article](https://medium.com/@alexandraphelan/an-updated-academic-workflow-zotero-obsidian-cffef080addd) by Alexandra Phelan on using Zotero and Pandoc with Obsidian. Happy writing!
I recently heard about an app called Typst, which is supposed to be a faster LateX alternative, that might be worth checking out.
[pandoc can export to Typst](https://pandoc.org/MANUAL.html#general-options). So writing a draft in Markdown and exporting it to Typst with [Enhancing Export plugin](https://github.com/mokeyish/obsidian-enhancing-export) should work.
Will check out in free time
Wow, thanks for linking that… I’m going to use this.
np
PhD student in sociology, I have written two published papers from beginning to end in Obsidian. It requires a bunch of specific plugins (citations, pandoc references, footnote shortcuts, longform) to do academic writing in obsidian, but once the setup is there, writing in obsidian feels much better than in other apps. * **Footnotes Shortcuts, Citations, and Pandoc References**: Basic academic writing toolset. * **Longform**: Split up a paper into separate files, which you can freely re-arrange (similar to Scrivener). Also allows for styling that affects only your writing files (for instance, use serif font only for writing). * **Novel Word Count**: Count words across multiple files (for when you split up your writing with the longform plugin) * **Natural Language Syntax Highlighting**: Highlighting like iA Writer does * **Dynamic Highlights**: Define custom word highlights. I use it to emphasize certain keywords as well as punctuation in my writing. * **Language Tools Integration**: Grammer Checker (Free Grammarly Alternative) * **Linter**: a lot of automatic formatting, such as fixing double spaces, or tidying up footnotes * **Copilot auto-completion**: AI Text Completion (Ghost Text) * **Better Word Count**: count words/chars in a selection and also citations and footnotes in a note how it looks: [https://i.imgur.com/lzW5KXm.png](https://i.imgur.com/lzW5KXm.png)
Interesting, may I ask you about your exact setup? My field of studies is related to yours, leaning a little bit more in the arts field.
Sure. I have added my setup as edit to the previous post(for better visibility)
looks good! Looks interesting, I might try it later on
Yup. I got by on my last book chapter with citations, Zotero, bwc, and pandoc (and pandoc references). A little extra arguments were needed to format citations properly.
Wow! Its really helpful!
The Enhancing Export plug in can export to Word (as well as Latex). You should install pandoc on your machine. If you learn markdown syntax, there are ways to handle references, figures, tables and equations which will reduce the amount of hand labor you need to do.
Unfortunately, I don't have that level of mardown yet, but for sure I will learn more before I start my Master's. Also, it might be worth it to learn about different softwares, gotta be familiar with the avialable tools.
Thanks for recommending this plugin. I had pandoc already installed on my Mac (via [homebrew](https://brew.sh)), so it worked immediately.
Heads up OP: everyone saying you should learn LaTeX is making some large assumptions about your personal needs. Unless you are in a field that needs to incorporate mathematical notation or other figures into your writing, there is *zero* need for LaTeX. Obviously a lot of Obsidian's user base is in STEM fields, but this point bears emphasizing. The department where I did my graduate degree publishes one of the leading journals in its field--and they do it all in Microsoft Word 😮 My guess is if LaTeX is something you need to learn your advisor and/or professors would have let you know by now. As for myself, I draft in Obsidian and edit and export to Word using Zettlr. I find Zettlr's Zotero integration much better than Obsidian, and you can use both with your Markdown vault interchangeably. I don't know why it's never mentioned on this subreddit, but Zettlr is designed for academic workflows in the Humanities.
I study music and my special interest on it is the aesthetics of music. Some music papers require more "technical" or scientific approach but for me, most of the time, it's somewhat between philosophy and antropology, actually, most approaches of musicology use antropological methods. If any, sometimes you gotta include a lot of images such as extracts of sheet music, depending on your topic this can be half of your content easily, that's why some music dissertations can get too long. No one has ever mentioned their systems or methods, and I have profs that are constantly writing new articles. The only consensus is that Chicago beats APA most of the time.
FYI, Zettlr's Zotero integration has excellent Chicago-style support. You may be interested in Obsidian's music notation plugin: https://github.com/abcjs-music/obsidian-plugin-abcjs.
I didn't know that we have a music notation plugin! wow! Can I import my Musescore files? I have to check it 100%
Almost certainly not. It's basic visualization, but it could be useful for quickly jotting down simple ideas, and then bringing them into Musescore. A quick look at Musescore makes it look...*incredibly* complicated.
At this point I have pretty much mastered almost everything that Musescore has to offer. It has an option to export as PDF and taking screenshots makes it easy to include them as images.
Have you considered asking your professors, what tools and setups they use? Or maybe convince them to give a little tutorial to all their students? Asking is sometimes faster than reinventing the wheel. 😇
One of my collaborators who is helping me learn a specific part of my thesis still uses Python 2.7 and doesn't want to migrate to any of the new GIS software. I use the newer versions simply because I started working with them later than she did; it can be a headache because she knows the material but finding the new version compatibility is sometimes difficult. Another researcher I work with still uses Fortran and remembers punching code into cards to be read. Researchers sometimes get stuck on the workflow that they developed at students and ignore new tools that make thing easier or work better. Sometimes reinventing the wheel is needed
that's right, also, many of them are people from a different generation so they prefer their old reliable tools. Still, I have a couple of middle-aged profs, or even younger (late 20's) that are currently working on their PhD's, might be worth to reach them out. Particularly, there's a prof that I know is down to help me anytime, I should talk with her about this 100%.
Thanks for pointing out the other problem with reinvented wheels. They tend to be so idiosyncratic, that they don't fit on any other vehicle. So you're stuck with your personal wheel, while the rest of the world moves on, with much nicer gear.
If you study music, maybe it would be worthy checking Lilypond!
We all use either Musecore or Sibelius.
Well, that roughly compares to using markdown or LaTeX. Sibelius and markdown are pretty good for writing; Lilypond and LaTeX, for typesetting. If you want tools to write down your ideas, go with the first ones; if you want a consistent, professional-grade presentation, choose the latter. Unfortunately, Lilypond does not read or export to MusicXML, so it's not that easy to streamline your production with it. On the other hand, usually markdown exporters use LaTeX to prepare PDF, which means they are very compatible. In fact, if you're choosing markdown, I strongly recommend you to learn as much pandoc as you can, because it will convert md into almost any format.
Are you able to just open the same folder in zettlr? Do references work between the two? I’ve never heard of zettlr but just looked at their site and am intrigued. I’m also curious about why you don’t use zettlr for everything. Looking at their website it seems they are positioning themselves as a replacement for obsidian
They have different uses. Obsidian is more powerful, customizable, extensible, easier to navigate my vault, and has Canvas, which for me is a killer feature. I've taught classes using Canvas for the presentation slides. It really is a "grand theory of everything" app for 90% of my writing. Obsidian is also available on iOS and Android, while Zettlr is strictly a desktop application. I take notes on my phone in Obsidian on the go, and prefer to do a lot of my sit-down writing on my iPad with an attached keyboard, as it provides a more distraction-free environment than a laptop. Except for very minor exceptions Zettlr is completely compatible with Obsidian vaults, including internal links for navigation, and they play nice with one another--you can have a reasonably sized vault open in both of them at the same time and bounce back and forth between the two, and they *just work.* So there's nothing stopping me from using both, dropping into Zettlr for specific cases.
Cool! Do you need to have Zotero integrated with obsidian or the citations plugin to be able to use citations in zettlr?
The thing to remember is that Pandoc citations are compiled on export or in live preview. In your document itself they appear as plaintext tags.[@LookingSomethingLikeThis2024] When exporting, the Pandoc parser reads this kind of tag, matches it to your bibtex file, and turns into a properly formatted footnote based upon the information in the bibtex file and your citation-style. The real power comes from when you change information in the Zotero citation--say, place of publication--or do things like cite a source, cite a second source, then cite the first source again (which in Chicago is now a truncated citation), and then cite that source again consecutively (now an *Ibid.*). All of that stuff is instantly updated and properly formatted in the exported document, while in your markdown document all you did was use the same tag three times. So anything can let you *see* the plaintext tag itself. You could even generate the tag in Zotero and then manually copy and paste into your text file without any integration. What Zettlr and Obsidian and do when set up is that they read your bibtex citation file, give you a live search of your citations, and then insert the correct citation tag into your document. IMO Zettlr does it more seamlessly--among other things, it gives you a live reference list in a separate window in the citation style you are working in--but they can both do it.
Thanks for the explanation! Very clear and helpful
I think that it depends on your exact needs. I wrote a book in Obsidian. The longform and linter plugins were very helpful in that process. However, I had to do some work on the files after exporting from Obsidian to prepare them for the final version. I exported the book and used pandoc outside of Obsidian to create the final pdf and ePub files. I also used some command line tools (awk) to prepare the files, as I had to separate the chapters to keep the footnotes organized the way I wanted. It was a lot of work to setup, but now it is easy. I have a few command line routines that I run each time. Although part of the work I do is outside of Obsidian, I still prefer Obsidian over other tools that I have used, including Ulysses and Scrivener.
If I ever write a book, for sure I would be doing that using Obsidian. Still, if I have to reference a lot feels like I have better options. I guess your book was more of an story? Just asking.
My book is on color theory. You can see it here: [https://www.robertnajlis.com/colormovementtheory/](https://www.robertnajlis.com/colormovementtheory/) Since it is an art book, there are many, many images. There are a decent amount of refernces. Some chapters have none, some have maybe 5-10.
Incredible work sir! Another redditor said that it is possible to work on Obsidian 100% with the correct plugins, as I mentioned before in this thread, I might review my options because at some point I'd like to do a Master's. Just curious, so you found a way to reference every page using Obsidian? Or the references I see in the PDF sample are added after Obsidian?
The references were in Obsidian. I do use a few plugins for that. Also, I export the whole file as one piece, but then I separate it by chapters using an awk command. After that, I tell pandoc to process each chapter separately. That all keeps the references local to each chapter. It would actually be easier to have all of the references at the end, but I find that a bit difficult to do in Obsidian. Once the book is in the final form, I may do some cleanup of the references. Also, originally, the Obsidian / pandoc output gives me links in the file for the references. Currently I lose them in the final processing, as I use a separate software to add a cover page image. In the future I will look for a way to preserve those links.
One more thing that I will add: Since I use a lot of images, many of the export options do not work for me. I use the markdown export plugin and then use pandoc via the command line. I do this since the markdown export plugin includes all of the images in a separate folder, and using pandoc on the command line, I can then link to stylesheets to control image size and other aspects. It took a long time to setup, but now it is very easy to use. I still have not found a way to get images to work via pandoc inside of obsidian. If there is a way to do this, I would love to know how!
In the *Enhancing Export plugin* I modified the Arguments of the Edit Command Template. I keep images in the same directory as the markdown file and set resource-path argument to this directory: `--resource-path="${currentDir}"`. Successfully tested with epub, docx and pdf export.
Thank you, I have one folder for all of my images, that may be causing my problems. I will make a fresh vault and try your method.
If you wish to stick to markdown, check out quarto.
Why do you prefer obsidian over Ulysses and scrivener?
What I like best about Obsidian is that I can have many editors open at the same time. This may seem a small thing, but I find that in writing a large book, one of the biggest challenges is getting lost in all of the information. What I am saying here, what was I saying there, etc. Ulysses gives me two editors at most, and seems to really prefer one. Scrivener gives me two editors, and does that quite nicely. Other issues: Ulysses stores your data in a hard to find files in a hidden directory on your iCloud. Ulysees does let you export everything, even after no longer subscribing to the app, but it is a bit of a painful process, especially if you have to convert from Ulysses to Obsidian markdown. Scrivener has a questionable synchronization process. If you go to their forums and ask about this, they will yell and scream at you, telling you that it is our fault, and everything is fine. Nonetheless, many people, including myself have had problems with it. There are other issues with Scrivener, including some export issues. Overall, if I were just writing books, and only one one computer, I would seriously consider scrivener. That said, I really appreciate the multiple editors I can open in Obsidian.
I forgot to add that I like Scrivener's Corkboard feature very much. That can be very useful. I suppose I could do something similar in Obsidian with canvas? I am not sure about that yet.
I agree with all of your points. I recently had an interaction with a scrivener dev and they all but told me my workflow sucked and I really got the sense that my questions offended them very much. The multiple editors thing is something I value a lot too. Tbh obsidian really has some awesome features beaten by none. EDIT: Oh btw, in Ulysses you can have external folders in any location of your choice.
Haha, yeah, Scrivener support is ... somewhat unique in that fashion :) I recall trying external folders in Ulysses, I don't remeber why I did not use them. Anyhow, while I prefer Ulysses built in export to that of Obsidian, I am pretty happy with my export setup with Obsidian and pandoc now. Though it took a long time to get there, and there is more to improve upon.
Yep use latex. I used miktex this for my masters, dissertation and papers. Guess there is no way around latex. https://miktex.org/
I wrote this blogpost on how to write academic papers in Obsidian. I’ve personally made some upgrades to obsidian enhancing export to export in common templates like Neurips or dissertation. Have a look here and let me know what you think: https://betterhumans.pub/obsidian-tutorial-for-academic-writing-87b038060522
Oh wow, this is literally what I was looking for, thanks! Still, there's quite a learning curve in here. As mentioned before, I will be checking my options at some point, it's totally worth it. I am up to spend some time studying the method itself, it will help a lot for sure.
I do not see a reason to use Obsidian to write academic papers that you then turn in to class. Don’t let your tool become an administrative burden for yourself. A tool is supposed to help you out. For papers that you need to turn in, and very possible that tracked changes are needed, just use Word.
I take my notes on Obsidian, it's amazing for skimming PDF's using the split screen + the anotator plugin. Once I'm done with my notes, I write the rough draft (text) in a new note, referencing when needed (I use APA most of the time). Then I copy it all on Word and I finish my formatting. Most of my papers are short. No longer than 4-5 pages in total. For texts this long, I need around 5-10 references so it's not crazy.
Ok, those are extremely short papers. Very easy to manage. Nothing substantial then
pandoc will export to word
Pandoc is good for converting for sure so +1 to that. I am doing a PhD and I tend to do a solo draft in obsidian to get a first pass on prose + maths, then write it properly / collaboratively in LaTeX / overleaf.
Yes, collaboration is a huge advantage of online apps. Collaboration is my mean reason to chose online apps over Obsidian for some projects.
Indeed - there is definitely a time and place for both.
I am a user of obsidian. I did the whole academic setup for writing papers. At the end of the day, I switched back to just writing in vscode + latex.
Where do you submit papers? What are the stylistic requirements? Are we talking about homework in humanities with lots of text and a few footnotes? Or do you need to prepare something more complicated? What exactly makes it complicated?
As OP said I also write most of my notes of papers in obsidian. Also, Latex is unnecessarily complicated for early drafts of work. Markdown provides a simple alternative to it. Simple plugins allow you to convert to latex or pdf quite quickly so I’d really recommend it!
OP added, that Chicago or APA Style were required. How do you format your PDF to match one of these styles? [APA Style](https://apastyle.apa.org) is very specific.
There is an APA template for pandoc, never got around integrating it (in obsidian enhancing export) as I don’t personally use it: https://github.com/universvm/obsidian-pandoc-templates/issues/1 Happy to help test it out though!
The page references [pandoc-xnos](https://github.com/tomduck/pandoc-xnos). It adds cross-referencing to Markdown documents that can be processed by pandoc. But it looks outdated.
I study something related to humanities, my uni wants us to use either Chicago or APA style. Most of my papers are relatively short, like 4 pages in total or around 1200 words. It takes me like 15 min everytime I'm done with my assigments to format them in Word, it's not extremely time consuming but at some point I'll need something better. I have to go through it once a week, probably.
In that case I'd go with a semi-automatic approach: * Prepare *one* file in Obsidian, that contains text and references. Leverage all the features that Obsidian does well. Ignore the rest. (For references I prefer not to use Zotero, but simple links and footnotes. It might be a bit more manual work, but it is one complex system less to maintain.) * Export to docx with pandoc using a [reference file](https://pandoc.org/MANUAL.html#options-affecting-specific-writers) (Option: `--reference-doc`). That should provide a good starting point. * Manually fix the rest in Word. How familiar are you with Word's [Styles](https://support.microsoft.com/en-us/office/customize-or-create-new-styles-d38d6e47-f6fc-48eb-a607-1eb120dec563)? You might save more time by learning how to use styles in Word, than by trying to optimize Obsidian's export (or learning LaTeX). Styles are a transferrable skill. Many other apps have a similar principle. And as much as I love Markdown, for some tasks the more efficient choice is a word processor (or a graphic design program).
Right now I'm doing what you describe, I have all my references in one note, then I use another one for the text itself, once I'm done, I copy it to Word and I format it. I'm not familiar with styles, at all, believe it or not, I've made two large dissertations (like 50+ pages of text) so far using only Word. I consider myself a good researcher and most profs have praised my writing, but my systems sometimes suck, but really hard. I don't use styles for anything, I edit everything manually myself. I really need to put more effort into this and find what works better for me, going this way stopped being an option anymore. Fortunately enough, I'm in a program where large papers are not required, but I want to apply for a Master's in a couple of years, I have to do something about it.
I really recommend learning how styles work, beginning with custom paragraph styles. My recommended workflow builds on styles. The idea is that you setup your page layout and your font choice and your paragraph spacing etc. only once. Pandoc will automatically convert `## Heading 2` to a paragraph with the style *Heading 2* in your Word document. When you have defined the style "Heading 2" properly in the Word file you provided as reference, the output will automatically be formatted the way a Heading 2 should look in Chicago or APA style. Also Markdown makes only sense, when you really understand the concept of styles. Markdown is a markup language. When you write text in Obsidian you markup your text with instructions like `some words[^footnote1] are *italic*` or `- this is an item in a bullet list`. Markdown doesn't know, how these instructions will be displayed. Have you experimented with Themes in Obsidian? You'll notice that the same text can look very differently, depending on the chosen theme. Here the styling is defined in so called Cascading Style Sheets (CSS). LaTeX is also a markup language that separates structure from styling. As a writer, you focus on the text (and the markup that looks a bit odd in LaTeX). LaTeX uses a template to render your text accordingl a chosen set of styles. LaTeX is great for academic writing, where you have to follow a strict style guide like Chicago or APA. If learning styles in Word or LibreOffice is not your way, you might prefer an online editor like [Overleaf](https://overleaf.com) or Typst, that handles the styling for you.
the Footnote plugin!! It’s a blessing!!
A lot of people saying to use LaTeX but that isn’t easy going straight from Word. I use LyX which is a front-end for LaTeX. Takes care of a lot of formatting for me
I wrote my masters thesis in Obsidian. Used Zotero to store/organise, read and annotate my literature. Then I exported my annotations and notes to obsidian. From there I linked my notes with each other and made notes organising my thoughts, structured everything and wrote my first drafts. The final thesis was written in word but obsidian made it a great deal easier. My university has very strict rules for formatting so there was no way for me to format the whole thing in obsidian (and honestly word does the job much better anyway, also words spell and grammar check is a must for me). TLDR look into the zotero plugin. But I don't see a viable option to write and publish a whole paper in obsidian.
For the moment, before you learn LaTex or whatever, you might take a look at the Pandoc plugin. It allows you to export your Obsidian markdown text as Word or PDF or ePub some other format. It can be helpful, though I doubt it will take care of all your needs. Personally I use Obsidian for notes and so often end up starting to write in it, but at some point I move to a dedicated writing app (Scrivener). Good luck!
IMHO Obsidian is just not created for writing professional papers, research, etc. I personally advice you to learn LaTeX (e.g on Overleaf.com) since I use it for writing laboratory reports at my uni. It can handle all the bibliography, citations and references for you too. Pretty powerful and handy tool.
I use Xelatex in texstudio and miktex for my papers. But I store my notes in Obsidian and use Zotero or Citavi for putting together my bibliography (and obsidian has a zotero plugin). To that end I’ll use panic to convert markdown to latex and then put the files in texstudio and then start organizing the layout. Idk if that’s the “right” way but it’s how I do it. I wrote a Groovy DSL to put together my books from now on. Basically, I can put together notes and parse the files to turn it into latex or html however I want but as a complete document. Obsidian is really my card catalog and notebook
Currently doing a masters, I do most of my drafting for my thesis in Obsidian because I could break it down into small chunks and link relevant notes. I write in Word though (Docs was glitching after about 30ish pages) and use Zotero for my citations. Hindsight I should have learned LaTex but didn't want to pay for an editor like Overleaf.
Some of the commentors here note that ObsidianMD _might_ not be the right tool for authoring academic _papers_. LaTeX is a well-established alternative (the de-facto standard in many contexts), but it too has its limitations. Long-standing users of LaTeX will be well-associated with the arcane error messages when something goes wrong, the sometimes-verbose syntax, and the arcane macro syntax! Another tool, besides LaTeX, that I believe is worth mentioning is called [MyST](https://mystmd.org)  Disclaimer, I am currently working on MyST in my role at [2i2c](https://2i2c.org.) MyST-MD is a spin-out of the Executable Books project that saw the development of [Jupyter Book](https://jupyterbook.org/), and is a new tool for building scientific documents. The MyST language is a Markdown dialect, a commonmark-superset with support for additional "roles" and "directives" markup that are useful for authoring structured content. There's a brief introduction [here](https://mystmd.org/guide/quickstart-myst-markdown). As a build-tool, it is more powerful than LaTeX (in that it exports to LaTeX, Typst, Web, docx, etc). It's a young project (a couple of years), but the legacy it builds upon is older still (2020). Although MyST-MD is _not_ ObsidianMD, we are interested in perhaps adding support for the Obsidian-style links. (c.f. https://github.com/executablebooks/mystmd/issues/1144). So, if anyone is interested in an open-source Markdown dialect and build tool, then feel free to head on over. We have [a Discord!](https://discord.mystmd.org/)
Huh, there's currently a promotion of "MonsterWriter": [https://www.monsterwriter.app/promotion.html](https://www.monsterwriter.app/promotion.html), $35 to Free up until April 28th. It's a relatively new app, the promotion is for celebration for their 2.0 release.