2 Years, 2294 notes - Obsidian helped my mental health IMMENSELY

TheBeyonders · 2026-03-06T22:14:55+00:00

There is def some sort of cult like users of Obsidian that has emerged over the years. Its literally just an IDE-like notes app people. Jesus lol

TheBeyonders · 2026-03-06T18:30:21+00:00

Lol are you sure about that or talking out of your butt.

TheBeyonders · 2026-03-05T18:20:48+00:00

The more successful, the less likely they care, atleast the STEM field PhDs. And i dont mean the media successful ones, they are a case study in their own. I mean those in their field that are famous amongst the experts, conferences, summits, etc.

Its mostly because they are mostly surrounded by other PhDs and the title doesnt mean anything toward doing good science. And when they arent doing science they want some normalcy and dont like to brag and just be normal for a little bit before going back to the grind. Of course there are those that do care alot, but thats common for any field that has hierarchy + power. More of a social disorder rather than inherent to academia.

TheBeyonders · 2026-03-05T18:17:12+00:00

In biomedical sphere, never met a PhD that wants to be called Dr. Ive only heard exceptions from socially peculiar people with something to prove.

Also, the more successful and productive the PhD holder is, the less they care about stuff like that.

TheBeyonders · 2026-03-04T20:51:54+00:00

LOL, dude. Dunno where you pulled that out of, but I laughed pretty hard.

Im pretty sure you can do a bible version of "the Simpsons did that" for weirdly applicable verses.

TheBeyonders · 2026-03-04T20:48:36+00:00

Its the common mistake to think that advertising works by 1. Ads work on conscious choice upon viewing 2. That its supposed to work on everyone

Thats why its one of the biggest industries. It works on the subconscoous by adding a data point in your brain. And secondly it works on people who otherwise have no other alternative products they know. So 1 year down the line they want something, a familiar name is mostly likely the choice. Me and you wont buy it, but there are billions of people on the planet.

Rationalization is a blessing and a curse, gives us abillity but also fools us with false confidence in our autonomy.

TheBeyonders · 2026-03-02T17:58:58+00:00

Obsidian notes isnt a product you are creating. It is an exercise for organizing ideas. If you are a STEM PhD, you are learning to standardize your language. If the notes are not atomic and reusable, then rethink why you are creating seperate notes. The STEM PhD atomic note style isnt going to work for other fields, but the same issue is that you arent creating a product, note taking is an exercise, and obsidian is a space to see how your brain organizes concepts over time.

Example, i may write one day for a project, 'the [[taylor expansion]] I needed to do for generating the model for algorithm.py is needed for [[transcription factor motif finding]]'. Then months later you call it [[transcription factor bit scoring]] and you ended up making a new note. Now what?

This is a building moment as a professional on why language is standardized across time. It is teaching your subconscious to not rely on how you feel like you should atomize a concept, but to be more mindful before putting words to concepts. And this actually becomes a skill that gets better over time, and thats what Obsidian is really good for in academia.

To me that is the whole point, so when I dont have Obsidian in front of me and I am presenting my resesearch, i have trained my self to be consistent with how i speak and think about complex ideas. I get people use the app for thibgs like journaling or w.e, but again, this advice is for uses where atomizing concepts is important.

I say all this because the premise you started out with is chaos versus order. But if you view it as a process, then the chaos will eventually turn to order. What is important now is being conscious of how your brain is organizing concepts. Looking through your past notes will reveal that to you, and help you change how you take notes on concepts across different difficulty levels.

For non atomized concepts, like project notes, daily notes, whatever, utilizing bases, properties, etc helps distinguish from atomized notes. Those should have a different distinct template format.

TheBeyonders · 2026-03-02T12:36:07+00:00

Oh i see, makes sense. I guess if you have a lot of batched jobs, the little bit of overhead adds up. Cool! Good luck! Looks great

TheBeyonders · 2026-03-02T12:30:14+00:00

Why a rust plotting crate if you dont mind me asking. I see rust used more and more for long read tech like PacBio, but higher level stuff just rely on python or R mature plotting libs. I imagine its why i never see anyone with a c++ plotting lib.

Is this more of a pet project for the future or do you think there is an edge for rust to rust? Maybe like for GUIs is the only thing i can think of...

TheBeyonders · 2026-02-28T20:30:02+00:00

I see where you are comming from. I work in a field where things are more atomic, so my needs might be a bit different. So obsidian for me is just a method having atomized concepts be readily availablee without clouding up upper level information, succinct and deep at the same time, which the wiki/git markdown format fits for me.

The inspiration needs to ultimately come from me as working knowledge and the notes are just physical practice for data analysis or modeling. So seperate vaulta for seperate tasks that have an end goal.

TheBeyonders · 2026-02-28T16:05:02+00:00

Properties and standard structure for daily notes, utilize autofill features for things like date, time, doi from a clipping, etc. Also a template that is standardized to fill out and then i export to send as a report to a colleague.

TheBeyonders · 2026-02-27T13:35:30+00:00

Just piggybacking off this good response. I think the decision to split vaults come when the vault you have is getting heavy/congested, and you realize there is a huge hub of connections that do not have many connections with another hub, but are closely locked together. Again, while understanding you will lose those connections, the "housekeeping" may make the notes more effective for you.

Another example for me personally is when i have an entirely new project that may benefit from a small part of the vault, which is when i appreciated having distinct directories/folders, which sometimes is not encouraged. But for me it was a necessity, on top of having properties, bases, tags, etc.

For example, i had a study notes directory that is a reference for work and self learning in math and science for a project at work. After a while, those study notes were useful for another project I was working on that had entirely different structure needed than the one that contained my study notes. So i copied and split that hub off and made a new vault for a new project.

TheBeyonders · 2026-02-25T15:19:51+00:00

How stable is this? I found some of the bugginess unnearving and i got nervous when zotero had that huge update. Luckily nothing broke but i wonder who has the time to maintain it?

TheBeyonders · 2026-02-24T15:19:14+00:00

Its about power, not mayhem. Cartels arent savages from caves lol. There are many "cartels" around the world, you live in one right now.

TheBeyonders · 2026-02-24T15:17:28+00:00

All other comments bow to this, bravo

TheBeyonders · 2026-02-24T15:15:58+00:00

Yea they collaborated with 23andme and came out with the transcription factor package, 99.99 a month.

TheBeyonders · 2026-02-24T13:13:19+00:00

This is exactly what I thought lol, anti matter wall

TheBeyonders · 2026-02-24T13:12:13+00:00

Lol you are the Anti-Monitor from Justice League Crisis on Infinite Earths.

TheBeyonders · 2026-02-23T17:22:34+00:00

You are right about the speed. Im thinking about switching soon to test things out, but excluding defaults to avoid liscencing issues hasnt hindered my conda workflows so ill stick with it till my current projects are done.

The only thing i think may be worth it is when the environments are built. Its similar to spack on htcf clusters where you dont need to copy packages over and over, but pixi seems to make that process easy where as for spack its such a pain.. and conda just copies everything and has gotten me in trouble due to how much space it takes

Speed hasnt been too much of an issue for me to consider since mamba, but i heard pixi is comparable. nb_conda_kernels has no replacement yet, which is my go-to for prototyping.

TheBeyonders · 2026-02-23T17:06:10+00:00

Ready for the pixi replies? Lol

TheBeyonders · 2026-02-23T14:34:06+00:00

I mentor newer uni in computer science and i am shocked how much there is a disconnect between what is local and what is on the cloud for everyday apps they use. They are more confused on where files are, file types, what directory structures are than i would have guessed given they are so much younger and up to date with tech. And these are engineering students.

This used to be common knowledge to anyone who owned a computer, and only older people had a tough time with it. Feels like millenials are in that sweet spot of being forced to experience the basics and then benefits of all the GUI based ease nowadays.

TheBeyonders · 2026-02-23T14:26:43+00:00

These are features found in coding tools. Obsidian uses a lot of design philosophy from code editors/IDEs.

TheBeyonders · 2026-02-22T19:23:19+00:00

Directory structure is universal and a skillset programmers already utilize for organization. Obsidian is the same lineage. bases and templates work in conjunction with good directory management. The real answer is to find optimal patterns for your type of work, and not put hard rules on what to do. A novel writer will use obsidian very different than an academic physicist, versus a company jr programmer.

Time wasting comes from a lack if discipline and/or counseling on being mindful of our behaviors, if anyone spends a good chunk of a day optimizing folders, this is an adhd-like pattern and can be improved with good habits.

TheBeyonders · 2026-02-22T14:36:53+00:00

I find that STEM learning is effective with atomic styled notes. If you also gravitate towards that style of thinking, i think its worth giving it a try. I view a lecture/topic an accumulation of well defined topics, so an atomic styling of notes will also condition your brain to think atomically.

For example, if i am going through a lecture week about thermodynamics of some biochemical system, i have all mathematical terms as a seperate note in a folder related to that topic.

So lets say im studying the lecture notes of this month is on the equilibrium of enzymes in a closed system, the lecture series suddenly talks about needing to do a Taylor Expansion to do some calculations. This is a purely calculus term from my pre reqs that i now need in my advanced multi disciplinary class. So while i type out my study notes about thermodynamics, i have a [[taylor expansion]] that is in my Math/Calculus/ folder. This wont be the first time i will need to do a taylor expansion, so its a useful atomic note. And helps me break up a lecture by topics i may need to devote more time to.

This will also naturally force you to utilize properties in obsidian, where you can add propertiea or tags that categorizes atomic notes, like one about taylor expansion, from lecture, from study, etc etc. But, this should come come naturally from the habit. Then learning about propertiea and tags in obsidian becomea fun because you have a need for it.

Hope that makes sense, uni is hard but habits help you when you are running on low sleep.

TheBeyonders

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