I always keep a notebook and a pen beside me when I am coding. It helps me keep a track of stuff and do a brain dump when required. What do you use? Like any specific application or good old notebook like me?
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Sometimes I draw flow diagrams or data structures on paper when I need to think how to solve a complex problem. I feel that when I need to think, nothing compares to pen and paper (or a whiteboard).
Besides that, I don't really take a lot of notes, nor do I use any fancy software for that.
I'm another fan of a good old fashioned notebook. I particularly reach for a notebook when I want to brainstorm something that needs diagramming. Sometimes I alternate between a whiteboard and a notebooks for a diagram, but I like to have a pretty good idea of what a diagram will look like before trying to render it on a computer.
More generally, I use the bullet journaling technique for notes. I've got a couple different index heading for notes (notes, architecture notes, ui notes, and programming notes).
When I'm brainstorming, I use Trello to plan things out, or my sketchbook for drawing wireframes or layouts. And when I find articles or concepts that are valuable, I save them to Evernote using the web clipper.
When I'm coding - especially something new, I keep all my notes in a new Trello card. Code snippets, StackOverflow answers, documentation links are all stored there thanks to the Markdown support and link attachments. Then I take my notes from Trello and expand them into blog articles using MWeb for longer-form Markdown writing.
Makes it much easier when I need to do complex processes again down the line, like configuring server software.
I always have a sheet of A3 paper between me and my keyboard. Pretty much all diagramming and note taking happens on that. When both sides fill up I grab another and put the old one in a stack for reference.
The older ones get binned once the info has been used for documentation, to-dos or are otherwise no longer relevant.
I alternate between paper notebooks + Quiver. Sometimes I use a touchscreen Chromebook running Squid as an "infinite whiteboard".
Nothing beats paper for speed of idea->representation. In my work, I find it best for the early stages of an idea, where thoughts are fleeting and getting them down fast counts most.
But, since we're coders, sometimes it's better to have a syntax-aware bucket where things can be copy/pasted or just worked out. That's what Quiver does for me. I also use it as a simple "knowledge base" that I can search for quick solutions to previous problems I've had. It's handy because it can do Markdown, LaTeX, code blocks, whatever, all in the same document.
I love Squid as an infinite whiteboard, and would almost recommend getting a tablet (or better, a touchscreen Chromebook that runs Android apps) just for this purpose. Some design problems just need to stretch out :) I tend to use this approach for ideas on which I need to iterate conceptually - because I can just keep moving to a different area of the "whiteboard" and try another approach, but then get a unified result. You can share the resulting document as a vector or raster image, and if you're a remote worker (as I usually am), you can join a videochat with the whiteboard open and screen-share it. This is almost as good as being in the room with a whiteboard!
I used to use complicated methods to keep track of what I'm doing, code, etc. but in the end, I use Notepad++ and markdown-style notes that I throw away when I'm done with a problem. This is at least for stuff I'm currently working on. It includes notes about how the system works and immediate todos.
Outside of that, and more formally, I use Paper at work for project discovery and to document how certain complicated systems work (such as calculations, and why they work the way they do).
I myself have a notebook handy and a small whiteboard next to my desk.
I don't use them too often though, only when creating something new or if I need some visual aid to reason through a problem.
I'm hoping to try Org mode soon, as I'm slowly learning emacs (vim user currently).
For development, I use notebook at my desk and whiteboards at my work (as well as at home). It's hard to come up with the clear plan for any challenge, so I do dump it down on the notepad/whiteboard.. Once I come up with the plan, I make short notes on text files on 'markdown' format. I take pictures of the whiteboard diagrams and add it to my notes. I save these notes to my bitbucket repo which I can refer any time.
I've tried a few different options (Evernote, OneNote, GoogleDrive, .txt file in Notepad) but always come back to just a little A4 plain-page notebook. There's something special about sketching out ideas on paper, don't know what it is but seems to flow better :)
I treat it as a unapologetic brain-dump, that gets thrown-out and restarted regularly. I've gotten the hand of self-editing what goes in the notebook (as it used to contain to dos, meeting notes, goals etc.) now its anything that I wouldn't mind being lost.
I definitely have to sketch out the tough things at least. There was a study I read about years ago that showed pen and paper were far superior to typing out notes. Something about the act of writing meant you were far more likely to retain the information even if you never go back and re-read the notes. I don't know if it's true, I don't know if it's even true for me, but whenever I'm feeling superstitious I make sure I write it down on paper.