Introduction

For a long time I used a particular set-up for my undergraduate studies. However, after I begin medical school in a few weeks, I’ll be using something different, and I think, superior.

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Below I will cover Joplin, MasterPDF Editor Free, LatTeX and Lyx, LibreOffice Writer, Stationary, Calendar, Contacts, and finally Email.

Joplin

Joplin doesn’t have a native PDF viewer. I had to use MasterPDF Editor which is covered below. Otherwise, I’d structure Joplin like the figure below, and it worked just fine for organization and regular typing—until it didn’t. I wanted to use either pure MarkDown, or Rich text. Though, Joplin has a button problem and any time a user would click the Rich Text button after writing everything in MarkDown, it’d break your beautiful MD formatting. The solution was to switch from Viewer mode to Edit mode, while disabling Rich Text Editor mode. Another annoying hiccup was that MarkDown view didn’t have PDF preview where one could scroll through the PDF, make annotations, or anything. So, I’d find myself clicking between the MD Editor and MD Viewer panes frequently—the side-by-side view is hideous. I got rid of Joplin, and imported all of my files to Zotero in a /University/* section.

University/
├ Psychology/
├─ PSYO 3001/
│  ├─ .Syllabus
│  ├─ .Assignments
│  ├─ Lecture 1

MasterPDF Editor Free

I’d use this in tandem with Joplin. I’d open PDF documents that I needed to edit (e.g. typing lecture notes down). It worked well, it was free, and I still use it. One cool feature is that it will always make an automatic backup of your PDF within your directory.

LaTeX, LyX

I used this for typesetting essays, and I wish I learned to use it sooner. I’ll continue using it.

LibreOffice

I used this for a bit, taking bullet point notes. I found it very clunky for studying as I’d either have multiple windows of LibreOffice Writer opened, or I’d be compiling enormous .odt documents.

Stationary

Paper: I used 90gsm printer paper for laser jets. If you go to Staples, it’s the second thickest pages you can get—they’re in the pink wrapper.

Portfolio: The cover was a folding plastic pretending-to-be-leather portfolio. I only loved it for the paper holder clasp. It kept the papers very still.

Pens: Kaweco {Steel, Brass} Sport, posted.

Ink: Kaweco, or Colorverse 84 (SM-1) and 85 (Costar).

Calendar, Contacts, Email

I used Baikal for my contacts and calendar, and it’s self-hosted on my server. For email, I used my Protonmail, and school email addresses in Betterbird. I’ve had zero problems with any of the software. By extension, my phone used DAVx^5 for calendar and contact syncing—the information is also available on my laptop and desktop

MD

I know, I know, I have to use Anki—and I will. Actually, I gave Anki a test-run in my 3000–level year and it performed so much better than I thought it would. I’ll say this happened in Genes, Brain, and Behaviour. When I began the course, I was feeling normal, but as the weeks rounded past the first month, we had midterms. Brainfog hit me in the middle of my exam, and I had it for a few days prior, too. I bombed the midterm, and I think I scored somewhere between 50% and 60%. This blew a hole in my confidence, and while I was balancing other courses, I needed to solve two problems: 1) figure out how to fix this brain fog before it’s too late; 2) get a high score on the next test to balance things out.

The brain fog question wasn’t too hard to answer, and that’s because the research was already published: The Potential New Treatment for “Brain Fog” in Long COVID Patients, 2022, Yale SoM. I read some other studies about neuroinflammation, NAC, COVID, and so on. After research gathering, I spoke to my pharmacist about taking the OTC treatment and I was told that it’d be no problem. So, I started taking NAC, and it felt as if a heavy wool blanket was lifted from my head, and I could take a cool breath of fresh air. Then, I turned to learning Anki.

Put simply, Anki helped me get a high-enough score to finish the course with an A-minus, but it took a lot of energy, and effort to ride the learning curve, while also learning new content. I used cloze and image occlusion for all of the slides, as this wasn’t a textbook+lecture+slides class, it was just a slides+lecture class, which I strongly prefer. It helps distill, and make easy to see what is testable. I find textbooks are far too broad, and with that generality in addition to time-constraints, people often hate the burden of three-figure length readings per week. I know I did. So, in medical school, I’ll be using Anki plus another few additions. First, though, let’s start with the new additions beause Anki is at the end of the river.

Zotero

Zotero is a well-known research assistant, that some people use with AI (more below). However, my to-be-used workflow looks like this:

Structure Zotero to agree with the names of courses that I’ll be taking in school.
Put in school files (syllabus, text, schedule, etc.) when available.
Annotate, highlight, and perform other manipulations in Zotero.
Export annotations to a note, and then copy/paste into Anki to make cards.
Record any accessory notes that aren’t related to Anki-style studying in the Zotero Better Notes plugin.

I thought about using A.I. to enhance my studying, and though I’ve criticized A.I. in an essay on this website, I wanted to see its capabilities. I downloaded OpenWeb UI, and hated it. The sole factor I was investigating was if I could use RAG (Retrieval Augmented Generation) to help me synthesize points from documents that I need to use for school. On one hand, I didn’t know if I was allowed to do this because of copyright, and other legal issues. My model(s) used in testing were all entirely offline, and open-source (ollama). Though, I did think that “If I am allowed to use this open-source program, and I am using a copy of a book that I own, how is it any different from me putting it in Anki?” That answer wouldn’t have to be answered after I tested RAG with a a 40gb corpus from my personal Zotero library.

It performed horribly—I scratched the project entirely. Also, anything that was to be directly used with Zotero (i.e. the plugins), the developers always chose to call the OpenAI API, or other paid-provider.

Anki

I’ll use Anki as I did in undergrad, but it’ll be supplemented with Zotero.

Laptop

I retired my Dell XPS-13 from undergrad, and gifted it to someone without a laptop. Of course, I put Arch Linux on it for them, too.

My new laptop is a Framework 16" and it’s been wonderful so far. I could go into the build (that I assembled myself), but that’s needless.

Dual Monitor

My dual-monitor set up, that I had throughout undergrad, was upgraded. I now have two 27" (monster) monitors, that are at 1080p. People may scoff at such a low resolution, when 2k, and 4k exist; however, 1080p is just fine and they were on sale. Plus I wanted large screens for reading ease. I sometimes find myself leaning forward to read, but this is a part of my comfort journey with my desk setup. The dual monitors are shared between my desktop and laptop.

KVM Switch

I got a KVM which connects my dual monitors to my desktop (plus a data cable), and my laptop. The beauty is that I can turn on and plugin in my laptop, connect the USB-C to dual-HDMI output cable, and use my desktop keyboard and mouse. This saves me such a huge syncing headache. Before, I had Joplin synced between my desktop (where I’d work on things mostly), and my laptop (that’d I’d bring to school), and phone (for personal notes). I hated it—so many replicas of a software I hated. Now the laptop set up is far easier to manage.

Data Back Ups

Backing up data is the final piece of the puzzle. I have server storage as shown below for backups, and other data storage. Of course, it’s all locked up with LUKS.

NAME         MAJ:MIN RM   SIZE RO TYPE  MOUNTPOINTS
sda            8:0    0   3.6T  0 disk  
└─evo        253:1    0   3.6T  0 crypt /var/lib/postgres/data15
                                        /mnt/sda
sdb            8:16   0 465.8G  0 disk  
├─sdb1         8:17   0   512M  0 part  /boot
└─sdb2         8:18   0 465.3G  0 part  
  └─root     253:0    0 465.2G  0 crypt /
sdc            8:32   0  14.6T  0 disk  
└─backup     253:3    0  14.6T  0 crypt /mnt/backup
sdd            8:48   0   3.6T  0 disk  
└─sdd1         8:49   0   3.6T  0 part  
  └─files 253:2       0   3.6T  0 crypt /mnt/files
zram0        252:0    0     4G  0 disk  [SWAP]

If you’re curious, here’s my backup script that I use for my operating system(s), from OS drive to external HDD.

Also, note how I kill zotero before I begin the backup. A constantly open database needs to be stopped before it can sync—otherwise corruption is a risk.

#! /bin/bash
killall -s SIGTERM zotero-bin;
sudo rsync -aAXH --delete --info=progress2 --stats --exclude=/dev/* --exclude=/proc/* --exclude=/sys/* --exclude=/tmp/* --exclude=/run/* --exclude=/mnt/* --exclude=/media/* --exclude="swapfile" --exclude="lost+found" --exclude=".cache" --exclude="Downloads" --exclude=".VirtualBoxVMs"--exclude=".ecryptfs" / /mnt/backup/Desktop-OS \
&& echo "The OS drive has been backed up."

Then, that backup is sent to the server

#! /bin/bash

sudo rsync -aAXH -e 'ssh -i /home/user/.ssh/user -p 1111' --delete --progress --stats --exclude=/dev/* --exclude=/proc/* --exclude=/sys/* --exclude=/tmp/* --exclude=/run/* --exclude=/mnt/backup/* --exclude=/mnt/Android/* --exclude=/media/* --exclude="swapfile" --exclude="lost+found" --exclude=".cache" --exclude="Downloads" --exclude=".VirtualBoxVMs"--exclude=".ecryptfs" /mnt/backup/* root@192.168.0.4:/mnt/backup/Desktop-Everything \
&& echo "The Operating System, and the SSD, stored on the external HDD has\
been backed up to the server."

Great! Now everything is backed up from everywhere, and onto a single place: plus redundancy!

That’s the final word regarding my school workflow.