The Academic Problem: mega-thread to come up with a solution

There’s a long-running thread here discussing ‘the academic problem’. And plenty of mentions of the term in other threads.

The ‘default’ JD system doesn’t work well for those in academia. You have more than 10 of some things, e.g. courses.

So let’s figure out a solution that everyone can use. I’ll document it as the first standard Johnny.Decimal system.

I need your help, because this isn’t a problem that I have.

Step 1: define the problem

Before we get carried away solving a problem, let’s make sure we all know what it is we’re solving.

Here’s an overview of what’s already been discussed.

  • @Al-Khwarizmi started it all and linked to an interesting graph, What does a Lecturer/Professor actually do?
    • And noted that “academic duties are typically grouped in a quite natural way into either three categories (teaching, research and service, as in the drawing above) or four (teaching, research, service and admin).”
    • And wondered “should research/teaching things be grouped by subject or by ‘kind of thing’? … Or is it better to have … the data, experiments, paper, reviews, etc. related to giraffes?”
  • @ks84 followed up with details of their system, which uses an extended number format.
  • @cidig posted another variant.

In a separate thread, @dan asked us to prevent him from using subfolders at uni.

@theTisch21 followed up with an amazing post detailing their SX.C.ID system.

So remember, we’re looking at this from both sides: as the teacher, and as the student. Are there any other perspectives?

I’ll tag @PhillyChuck, @LasTr, @jden, @trevortds as others likely interested.

Request: describe specific issues or requirements

So the request for the next week or so is for everyone to define, in this thread, their specific issues or requirements.

Tell us about the structure of your work. Why doesn’t it fit in to JD. What does it look like.

Be specific! This is the time for details.

In about a week – say Sunday 2nd June – I’ll consolidate these responses and we’ll move on to the next phase.

Try not to solve the problem yet!

We’re still in requirements-gathering phase.

Would a Zoom session be helpful?

I’m very open to hosting a Zoom session here, as long as it would be structured and helpful. I say let’s see how this goes for the next week, then make a decision.

Happy to hear your thoughts. Spam the thread!

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First of all, very nice way I think to brainstorm a solution as a group.

I am a student myself and structuring courses can be though, because in my structure, the degree is my ID. So a bachelors in Accountancy in my system is:
30-39 Knowledge/36 Education/36.03 BSc Accountancy

This means my courses in this degree are subfolders and if more structure is needed within a course more subfolders are needed. So some course documents are two levels deeper than my ID.

But I also like having my degree as an ID. Because, once a degree is completed I do not want these higher up in my structure as area of category. But I want to keep these documents as reference.

That’s my education problem statement. Keep in mind, I do not have a full student structure, but it is embedded in my complete personal JD-structure.

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Excellent! This is exactly what we’re looking for – all the different situations and setups to consider. :+1:


Thanks for putting this together, Johnny!

Like the previous posters have mentioned, the four buckets of things that I do in my daily work are research, teaching, service, and admin (in order of importance, with research being the most important but often the one I seem to have the least time for). I think JD excels at handling service and admin work (committee meetings, forms, and other bureaucratic miscellany), but it is very rigid in terms of being able to luxuriate and explore your ideas since the index structure is quite strict. Because of this, most of my “thinking” materials live outside my JD system — PDFs of all the articles and books I read reside in Zotero, with folders for specific projects (and the same file can live in multiple folders without being a duplicate), notes (from seminars, while reading, random idea that should make it into a paper) live in an Obsidian vault that stands alone, and paper drafts (since they can go in and out of revision based on where it is in the review process) liver in Overleaf mirrored into GitHub repos.

I think what JD misses for me with the “thinking” materials is flexibility and discoverability — in my brief dalliance with PARA, I realized that PARA theoretically prioritizes ease of discoverability (which comes at the cost of organization) while JD excels at ease of searchability. (Happy to elaborate more on the distinction I’m drawing here.) When it comes to managing syllabi, student homework, meeting agendas, JD works like a dream. However, I’m stuck when I try to think about working with it as a way of generating lots of new ideas (or synthesizing them across lots of domains) — sometimes ideas can and should live in lots of different places, rather than a single folder in a single box. The best parallel I can think of is the differentiation that Obsidian makes between folders and tags — tags allow me to keep notes in a way that’s linked to multiple things, so I might be able to find hidden connections between ideas that I might not have thought of, but I am wary of using tags too often because I know that that can explode into a mess that I won’t be able to JD easily. (For this reason, i haven’t really used tags until more recently.) So, my main issue with JD for research is that it doesn’t help me organize my thoughts in ways that help me make connections across lots of different notes, since they often sit in their own little silos.

As for teaching, I have addressed this by having classes listed as categories. My university does all classes with numbers only (eg, introduction to X might be 1.0001, then 1.0002, and so on), so that doubles as a consistent file name convention. To differentiate between different semesters, though, I’ve resorted to listing classes as I teach them: 21.01 Class 1 (spring 2024), 21.02 Class 1 (fall 2024), 21.03 Class 2 (fall 2024). This means that I still might have one additional layer of folders that I consider “tabs” — HW1, HW2 for homework or L01, L02 for lectures) but I generally just try to have the file name do most of that work rather than relying on subfolders. One thing that would be helpful for thinking through with JD is being able to create “templates” (which I know was sort of covered in the workshop) — with classes, for example, it’s useful for me to have a “template” for each class folder especially since the lectures only change incrementally year to year. This is similar to the problem that creatives face, I think, so I’m looking forward to seeing how this gels with other forms of creative, open-ended work as well.

Those are my two main issues I’m dealing with now but I’m sure more will come to mind as other folks chime in!


JD - as a senior professor, here is one problem. I’ve defined area 20-29 to Teaching. Each category represents an individual course I’ve taught, and within each category I have put in a separate ID for each time that I have taught the course (regrettably, I need to have subfolders in each ID, for example for each class and each exam - so I’ve violated the strict orthodoxy).

But as you can see, I’ve essentially run out of categories for any other courses I might wind up teaching on a regular basis. Per one of your videos in the workshop, this might be a usecase for expanding the category “namespace”. This is a bridge I may need to cross, and not sure what the solution is.

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Can you help us here by telling us more about the structure of those courses, how many there are, across what timeline, if they have their own natural method of organisation, and so on?

It looks here that ENVE422 is a class/course that you teach across years? Is there a higher structure that we’d need to consider, e.g. ENVExxx sits within Environment sits within Geology?

These are all pretty much courses within my department (ENVE is environmental engineering, and I am in a department of Civil, Architectural & Environmental Engineering. What we call departments in the US are often called schools in Australia). Within each course offering, I tend to have one folder for each lecture and each exam. There are three or four courses I have been teaching for many years, but there are others that pop up that I need to do as new efforts.

I can imagine that some professors might do four or five different courses in an academic year.

Plus to make this even more “interesting” we may be embarking on a curricular modification which will result in new and different courses.

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I think you have summed up exactly the limitations i have discovered with JD. Which is that it a rigid file organisation system. This is why I’ve made peace with using JD for everything where organisation is what i need. But for my thinking notes i rely on backlinks and search.

On a side note, can you please share how you use devonthink? I have it too but i feel that i don’t use it well. Happy for you to start a new thread.

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+1 on showing the DEVONthink workflow!

As a separate thread pretty please! I’d like to keep this one focused on this specific problem.

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I’m a mathematics graduate student in the US. I’m in the process of implementing JD to organize my files but have found that is the best way to organize my notes. I tend to fall for the subfolder trap when it comes to organizing my vaults. I believe JD is a good way to mitigate that, but .

An issue that arises is that there are many types of mathematical objects and many more ways for them to interact with each other. This is where is really able to shine. As far as tags and links go, files are tagged with names like definition, theorem, or a more utilitarian hidden. I use plugins that run Javascript to determine what kind of note I’m creating.

Another issue is figuring out how to effectively context switch between day-to-day file organization and the open-ended nature of I plan to use a “canonical” version of JD to organize my computer.

There are two ways that I’ve thought about doing it.

One vault using JD to organize it

00 Meta
   01 JD Manual
   02 Etc.
10 Admin
   11 Home
   12 Auto
   13 School
   14 Etc.
20 Work
   21 Etc.
30 School
   31 Notes # Obsidian vault; JD
      310 Info
         3101 Subfolder containing scripts, meta data, tags, etc.
      311 Atomica # Definitions, theorems, etc.
      312 Etc.
   32 Assignments
   33 Financial Aid
   34 Etc.

Or, multiple vaults using JD to organize them

00 Meta
   01 Etc.
30 School
   31 Subject 1 # Obsidian vault; JD
      310 Info
         3101 Subfolder containing scripts, meta data, tags, etc.
      311 Atomica # Definitions, theorems, etc.
      312 Etc.
   32 Subject 2 # Obsidian vault; JD
      310 Info
         3101 Subfolder containing scripts, meta data, tags, etc.
      311 Atomica # Definitions, theorems, etc.
      312 Etc.
   33 Assignments
      331 Course 1
      332 Course 2
      333 Etc.
   34 Financial Aid
   35 Etc.

I would prefer to keep all of my notes in a single vault. Assuming consistency, it wouldn’t be too difficult to compose a singular vault from multiple, but I’d like to avoid that if possible.

My current Obsidian vault looks like this:

   alternating group on n letters
      book 1
      book 2

Note: this is for a single subject.

This is what my first vault looks like:

   Images and GIFS
   Dataview # a plugin
   Organization # organizational scheme for the vault; a joke
   To Do
      School 1
         Course 1
         Course 2
      School 2
   Public # this is linked to my GitHub for sharing; currently not in use
      Source 1
      Source 2
Planner # contains Dataview (a plugin) tables with assignment information and a calendar

As you can see, this is a mess… and not fun to manage using Javascript.

Excited to figure this out!



As a student, to me, the fundamental issue is that classes naturally benefit from subfolders, but we always have more than 10 classes. Those constraints prevent you from both having a class as a subfolder-less ID, and a category. Even if you use categories that span several areas, that adds up to a significant amount of category space taken up. I haven’t used more than 10 IDs in a single class yet, so a whole category per class would feel like wasted space, especially when you’ve only got 100 to work with.

My Requirements

  • Support more than 10 classes
  • Allow classes to have additional organization (sub folders) that are structured
  • Organize either by subject or by the time the class was taken
  • Allow for sufficient organization outside the class structure - at least 3/4 “normal” areas

How many subfolders would you typically need in a class? Just as a rough guide?

And how many files? Could you send us a screenshot perhaps?

JD - if this helps, here are the “internals” for a single JD ID for a class from 2023 to illustrate the complexity

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Okay so the types of thing we have here are:

  • Class (can you explain 1A, 1B etc?)
  • Syllabus
  • Exams
  • Ideas/outlines
  • Surveys?
  • Diaries?

Some of those feel personal, i.e. not necessarily standard?

This is all good, please keep throwing all these ideas out here. I want this all to mix around in our brains and when we’re comfortable that we’ve captured it all, we’ll move on. But not yet!

Remember, no wrong or bad ideas here. Brain dump.

1A, 1B – the number is the week (we have 10 week terms) and the class meets twice a week (A/B) - I settled on this numbering scheme years ago.

Correct - a mix of lecture materials, exams, diary (notes for next time) and other dataa

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  • Syllabus/meta
  • Notes - I’m using Obsidian, with varying structure of MD files. I do use subfolders a lot here, but it keeps my notes organized, and I personally don’t feel like each note/folder needs it’s own ID.
  • Small assignments (ones that I can keep to a single word doc/powerpoint/other). Things that don’t warrant their own ID because they’ll be done in 30min.
  • A folder for each large project. There’s usually between 0-3 per class, so let’s say 3-6 “things” per class to organize. I had one class with a few medium assignments, total of 8 IDs used.

Files vary drastically depending on the projects, I’ve got IDs with 10 files (drafts, final drafts, and follow up documents) and IDs with 2 (the same idea just in two different formats). Two screenshots below of one example class: one is a “tree” command output of that class, and one with just all the files put in one big folder. Hopefully that gives a sense of the structure and the files I’m trying to organize.


(Yes, I did use a subfolder. It was one assignment that I had already completed, but needed to export it as 2 different formats)

Hello Everyone!

Just as a quick introduction because I am very new here, I am a first-year student attending University this semester, and I have been getting into organizing my life. I stumbled across OmniFocus, which snowballed into me finding Obsidian and finding different ways to organize my notes and my ‘second brain.’ I was reading up on JohnnyDecimal and love the visual organization and numerical system. I found this thread while pondering how to organize my vault further than the normal 0-10 > 0 > 0.01 system, and I came up with this fairly simple idea that I’m sure people have shown before. I have no idea what the limits are, but I can’t imagine I’ll have too many different files to put in per semester, and if I do, I can move things down a level.

I do not know if this is considered sacrilegious, but I am trying to make it work for me! The only realistic problem I can see with how I have it set right now is if I need more than 10 per sub-sub category, but I imagine I can do something along the lines of 10.100, 10.101, 10.102, etc. The system will get quite large if need be, but thankfully, that’s why I have a notes app, so I don’t have to keep it all in my head! I have decided against ID’ing text files and will only do it on folders (to keep it as simple as possible for now).

I’d love any feedback or suggestions on ways to improve, as I am very new to this atmosphere of personal organization and note systems.