Threads for jkanche

  1. 1

    what was the reasoning to use a home grown solution that use something like Lit-Element or Lit-HTML ?

    1. 5

      With all the enthusiasm for zettelkasten/second-brain like systems (roam, org-roam, now this), I’m surprised that nobody has been working on I haven’t heard of an external format/tool that various UI’s can interface. VSCode, at least that’s my impression, is the kind of editor that gets displaced from it’s throne every few years by the next new thing, as has happened to Sublime and Atom before, so I certainly wouldn’t be too confident in making my “second brain” depend on it, except maybe if it’s used as a brainstorming tool for projects, but then it would have to be distributable too – but from skimming the article that doesn’t seem to be the case.

      Edit: Fixed the first sentence, sorry for my ignorance. Also I missed that this is markdown based, so I guess the rest of the comment isn’t quite right either, but I guess/hope my general point is still legitimate.

      1. 6

        I’m surprised that nobody has been working on an external format/tool that various UI’s can interface

        Checkout neuron which is editor-independent, has native editor extensions, but can also interface (in future) with editors through LSP.

        Some examples of neuron published sites:

        Easiest way to get started (if you don’t want to install yet): https://github.com/srid/neuron-template

        1. 3

          That sounds cool, but I don’t really get why LSP would help? I (personally) would much prefer a native client, in my case for Emacs, than something that forces itself into a protocol for program analysis.

          1. 2

            Well, neuron does have native extensions for emacs and vim (see neuron-mode and neuron.vim) - but LSP support just makes multiple editor support easier by shifting common responsibility to a server on neuron.

            EDIT: I’ve modified the parent comment to clarify this.

          2. 1

            Is there any easier way to install (i.e. without nix?) I’m on a laptop and installing new toolchains is prohibitive for the low storage I have.

            1. 1

              Nix is the only way to install neuron (takes ~2GB space including nix and deps), until someone contributes support for building static binaries.

              But I’d encourage you give Nix a try anyway, as it is beneficial even outside of neuron (you can use Nix to install other software, as well as manage your development environments).

              1. 2

                I got a working binary with nix-bundle, that might be a simpler option. It’s a bit slow though, especially on first run when it extracts the archive. nix-bundle also seems to break relative paths on the command line.

                1. 1

                  Interesting. Last time I tried nix-bundle, it had all sorts of problem. I’ll play with it again (opened an issue). Thanks!

          3. 3

            Isn’t the markdown that this thing runs on exactly that external format, and one that has been getting adoption across a wide range of platforms and usecases at that?

            1. 3

              There is tiddlywiki and the tiddler format.

              1. 2

                I wish the extension used the org format instead of markdown (so if something happens to vscode, I can use it with emacs), but otherwise I totally agree with your comment!

                1. 2

                  You can use markdown files with org-roam in emacs by using md-roam. I prefer writing in Markdown most of the time, so most of my org-roam files are markdown files.

              1. 5

                One thing I’d be curious to know from others is how do not get overwhelmed by your own systems. I have a lot of difficulty organising things and frequently forget where I put things.

                Lately this has led to a workflow where I have two text files. One where I put what I ought to be working on today, and a second one I euphemistically call “the scroll” which is just a long file I append notes to as they come. But I like the idea of something where I schedule my day and keep track of next tasks. But I worry about committing to a system where tasks get buried across files under some subheading that org-mode might be hiding from me at that moment.

                1. 3

                  This is exactly what I do, but just with orgmode. todo.org and journal.org (and archive.org for things coming out of todo.org). I sometimes try to schedule things with org-agenda, but inevitably something will take more time than I expect and I get off schedule. So, I really only use org-agenda for true deadlines. It’s really quite simple. As you said, if the organization system itself gets too complicated, then it breaks down.

                  1. 1

                    Thanks! I think I’ll try to turn the scroll into a proper org file and slowly migrate into something that uses org-agena

                    1. 2

                      Something that’s really important is good org-capture templates.

                      Here’s the line in my config where I define my org-capture-templates: https://github.com/wraithm/emacs.d/blob/dc49776342df4b75c732d8e27647c751d1043a48/lisp/init-org.el#L46

                      I’ve actually since moved on to doom emacs with slightly different capture templates, but that’s a good example of org capture templates that work well for the system you described.

                      1. 1

                        How well do org-capture templates handle large notes? Like I cut-paste large chunks of text into my scroll. Whether it be snippets of websites, emails, or conversations.

                        1. 2

                          Yeah, it can handle arbitrarily long text afaict. The capture template just opens a buffer with the node that’s gonna get inserted into your org file’s tree. It sounds like this is exactly what you’re looking for. The capture template is just for giving you automation around how the snippet that you want inserted into your scroll gets formatted and categorized.

                          1. 1

                            it does handle large text pretty well. org-capture is for quick short term storage. I move these eventually to other org files based on context. (using org-refile)

                    2. 3

                      Use org-mode with org-agenda. Here is one of many guides showing a workflow using org-agenda, but the point is that if you spread your stuff across many org-mode files, org-agenda will be your “dashboard” into those many files so you don’t have to go hunt through files and subheadings to find todos and so on. Instead it presents the data, scattered across many files, in a single, coherent view.

                      1. 1

                        So one issue I had is that there is my file where I keep all my tasks, and then the file which where the work for the task that needs to get done. How should that be stitched up in org-mode? Do I put the TODO and Schedules in my org file that has the tasks and link from that line to the file where I do the work?

                        1. 2

                          What do you mean by “and then the file which where the work for the task that needs to get done”? Is that file another org-mode file which describes the work in detail, or is it like a file in a software project or something like that? If it’s the former, I suggest putting the todo in there. If it’s the latter, I usually put a “org-mode link” to the file (and location in file) in the todo.

                          I have a “todo.org” file where I have todo’s that doesn’t fit in other places, but I also have todos in a lot of other places, and then I keep tap on them all with org-agenda.

                          1. 1

                            I meant the latter. Like I have a todo around expanding out a section of a paper.

                            1. 1

                              I’m still not sure I follow. Can you show me an example of what the two files can look like?

                              1. 1

                                Sure suppose there is a file work.tex:

                                \section{Background}
                                Lorem Ipsum
                                

                                And I have a file tasks.org

                                * Do grocery shopping
                                * Flesh out Background section of paper
                                * Water plants
                                

                                You would have me modify tasks.org to have:

                                * TODO Do grocery shopping
                                * TODO Flesh out Background section of [[/dir/to/paper/work.tex][paper]]
                                SCHEDULED: <2020-05-27 Wed>
                                * TODO Water plants
                                

                                Does that sound right?

                                1. 2

                                  I think in that case, where the link is that “broad”, I’d replace the TODO-item with:

                                  * TODO [[/dir-to-paper-work.tex][Flesh out background-section]]
                                  

                                  the goal being to quickly go to where the actual work of the TODO-item should actually be done. Had there been more steps, I’d maybe have a TODO with subtodos that link to different parts. And in the event that the TODO-item expanded so as to justify it’s own org-mode file, I’d mode it all there. If you just make sure to tell org-agenda about where to look for your org-mode files, it will collect all the items from all the files, so you can have as many or as little as you need.

                                  1. 1

                                    Thanks! That clarifies a bunch.

                    1. 2

                      ever since I started using org mode and spent some time to really understand (the basics) how emacs and the ecosystem works, its been a pleasure to use it. Its an incredibly powerful system, and no web app can replace it. unless you want portability but you can store/sync you org files with google drive/dropbox!

                      1. 2

                        This is neat!

                        This reminds me of an similar looking emacs theme.

                        1. 1

                          I’m not in that field, but wow, that’s a devastating response. I guess this competition is good for bioinformatics, though?

                          1. 1

                            Implementation of algorithms varies a lot depending on how experienced/efficient the programmer is. I think the bigger picture is what the seq language tries to solve. the comment by the author of the seq paper on the article makes this more clear

                            I think the main benefit comes from our higher-level constructs/optimizations like pipelining, prefetching or inter sequence alignment, which are difficult to replicate in a library. And we’re just at the tip of the iceberg here – there’s a lot more we’re excitied about exploring, including different backends like GPU/FPGA. One of the reasons we built Seq was to be able to explore these kinds of things in a systematic way, and I think that’s where the value is

                          1. 1

                            Not sure if this fits everything you listed but here’s the links -

                            wrk - https://github.com/wg/wrk wrk2 - https://github.com/giltene/wrk2

                            1. 1

                              My current (as of 2011) website is https://f5n.org - I used to blog a lot more, but for the last few years I’ve neither written “journal style” posts nor technical content like I used to. This is not my first blog and not my first website.

                              Interesting decisions regarding the technology stack

                              Nope, nothing interesting here. I wanted to use a static site generator after using several homegrown CMS and blog things in several languages for 10 years. So I used something that sounded useful (Hyde) then migrated to hugo a few years later. Still running hugo as of now.

                              I do want to add some indieweb stuff (micropub), so we’ll see how that works out, needs a dynamic endpoint after all.

                              I do use Twitter and I want to put small blurbs on my own website. Same for those few Instagram posts I make per year.

                              1. 1

                                very cool! I love the style and simplicity of your website!

                                1. 1

                                  Thanks, I know I’m really not good with designing things, so I’m already happy if it’s not too garish.

                              1. 1

                                Mine’s pretty simple and minimal. I use hugo and a modified version of the hugo-xmin theme. I hope to write/start a blog at some point.

                                website : http://jkanche.com

                                theme: https://github.com/yihui/hugo-xmin

                                1. 1

                                  I use trillium notes, as it offers tons of features for linking and organizing notes and has markdown support as well.

                                  1. 1

                                    looks very Interesting! Does trilium use plain text (seems like it uses sql-lite ?)

                                    1. 1

                                      Yeah, it uses a database to store all the notes, which allows it to handle a large number of notes quickly. It does give the option to export all the notes markdown if you need to edit them elsewhere

                                  1. 1

                                    I really expected Notion to show up in one of these responses. Maybe it’s not quite the thing for the Lobsters crowd, but it seems to fit exactly this role: it apparently can set you up with a personal wiki, daily journaling, and project management stuff really well. I haven’t used it myself, but I keep hearing that it’s pretty good – I’m just kind of afraid of the total buy-in it seems to require.

                                    1. 2

                                      I’ve tried Notion before. Although I like the tool and constantly hear about it from others, I think it suffers the longevity problem (checkout the longevity statement from standard notes). Last i checked sync to a google drive or dropbox is missing, and their export to markdown is super basic at the moment with a lot of issues.

                                      1. 2

                                        For sure. That was part of my thinking when I was trying out Notion too – I have to take the time to set it up, and then I have to truly believe that it’ll be the right thing for me long-term. Evernote’s slow demise has sort of eroded my trust in proprietary brain-dump tools.

                                        longevity statement from standard notes

                                        Here’s the link for anyone who, like me, hadn’t heard of this before.

                                    1. 1

                                      A mishmash of:

                                      • nvalt+simplenote(tickling)
                                      • markdown files in various folders (journaling + more formal notes)
                                      • pinboard (usually website notes quotes)
                                      • trello (todo lists)

                                      I’ve been trying out Roam this past week to replace the second bullet for journaling + booknotes. Enjoying it though am currently fighting between it and pinboard when it comes to website notes.

                                      1. 1

                                        I like roam but personally i would like to use a platform that can sustain in the long run. I can see open source tools having a longer life than a web based tool.

                                        1. 1

                                          I’m having a bit of trouble understanding your comparison of “open source tool” and “web based tool”. I see it as just a sea of tradeoffs as someone who both pays for tools I depend on and spends time learn/contributing to open source tools. I’m hoping roam largely grows into something with some pdf/web archiving features, something I already am used to paying for despite knowing I technically could do the same thing in a self-hosted manner.

                                          Sleuthing through old bookmarks, I did see a windows app called ConnectedText with the same double-linking feature, but it’s been abandoned from what I can tell. Calca could be seen as another example (it’s falls a bit more in line as a text editor rather than something with databasey features), but again, the app is seldom maintained (in some sense, it’s reached a state of completeness but there’s some bugs I’m not sure I’ll ever see fixed in it).

                                          Conor & Tiago talk a bit more about business/app abandonment here: https://youtu.be/Hw2kJF_kxjE?t=2733

                                          1. 1

                                            what i meant was, I would be more comfortable using a tool for the next 10 years or so without having to constantly worry about when its gonna go offline (I hope roam doesn’t and gets big). If its open source, even if i pay for the tool now, I know that sometime in the future, I can continue using it.

                                        1. 2

                                          Do you use org-journal ? Do you mind describing your workflow ?

                                        1. 1

                                          I used to use Orgmode for my work logbook (with org-journal), but I switched to Agenda because I wanted something that supported both handwritten notes on an iPad (something I find I do a lot now in work meetings) and typed notes on a desktop (Orgmode obviously only does the latter).

                                          Agenda isn’t perfect: its editor pales next to emacs of course, and I wish it had better outlining support (it just offers word-processor-esque indent/outdent). However it is simple enough, and date-focused enough, that I find it makes an excellent logbook.

                                          I still use Orgmode for my non-logbook notes and all my other writing though.

                                          1. 1

                                            I wish i had a mac, I love Agenda and Things

                                          1. 3

                                            I am currently experimenting with TiddlyWiki and its journal feature which has a stated goal of being self-contained and staying usable for the long term. And has many options for storage.

                                            1. 2

                                              What mechanism do you use to save (and sync across machines) tiddlywiki pages?

                                              1. 2

                                                I would be interested in this as well unless op is thinking about using a hosted tiddywiki instance.

                                                1. 1

                                                  I have Caddy with the webdav and jwt plugins. It works great until the jwt expires, so turning off autosave is a must.

                                                  1. 1

                                                    I am still experimenting. Right now I use the node based server on my laptop, running against a data directory in a Dropbox folder. But this is more for backup than sync.

                                                    1. 1

                                                      My ideal case would be any solution that involves each save directly writing to the local file (a Chrome extension, perhaps?), so I can just sync that file in Keybase filesystem, and get automatic sync as a result.

                                                  2. 2

                                                    a lot of people complain that tiddlywiki becomes unusable once you have too many tiddlers. I’ve tried it out and it works but i’m backing out for this reason

                                                    1. 2

                                                      This is what I currently use but the task list plugin does not provide some of the features I am looking for. I wish it was more along the line of org-agenda

                                                    1. 1

                                                      I wonder what you hope to accomplish with the journal?

                                                      I make use of Simplenote (https://simplenote.com/) to jot down quick notes. It is open source and has desktop apps across Mac/Win/Lin, native mobile apps, and an API that someone has nicely wrapped up for vim. The company behind WordPress (Automattic) has committed to running it as a free service.

                                                      But I don’t really use it to keep a “journal”. The closest I come to that is that for the last ~4 months, I track all my working time in about 10 categories (e.g. Meetings, Code, Inbox Zero, Planning) using the proprietary (free) tool Toggl, which is like a SaaS synchronized stopwatch with native mobile / desktop apps and a simple reporting backend.

                                                      1. 1

                                                        I’m thinking more along the lines of journaling and dumping all my thoughts like a second brain. Its not just for work but also for personal things.

                                                        1. 1

                                                          Gotcha. You may find Simplenote a good fit; its main advantage is its simplicity (it’s just a cloud-synced folder of plain text files), its ubiquity (native apps everywhere make it easy to quickly jot stuff down), and that even though it is open source, it’s also fully hosted for you. There’s also markdown support, optionally per-file, and the ability to publish notes. But since it’s just plain text, it won’t assist you any way in the actual journaling technique, and doesn’t support any inter-linking between notes. I usually find that stuff is “YAGNI” material anyway.

                                                      1. 11

                                                        Two answers: for a lot of things, I use jrnl. Easily allows you to have multiple journals and easily outputs markdown if you want, and lets me use my editor of choice. And the tagging system makes it easy for me to notate if I’m making an entry about a particular problem I solved or issue I hit, which in turn makes it easier for me to find that information again if I hit similar issues/need to reference it.

                                                        The other thing I use heavily though is a reThink tablet, where I just write out longhand. That works better when I’m trying to sort out my thoughts. jrnl has generally been more helpful for me when I’m truly trying to log stuff.

                                                        1. 1

                                                          This looks super nice! I did not know about this before!

                                                          1. 1

                                                            Looks nice but seems like it’s unfortunately broken for Mac. Installed via home-brew but it seems like it’s incompatible with the Python version supplied by home-brew (3.8).

                                                            1. 2

                                                              It’s not broken on Mac; it’s broken on Homebrew, and that only since late last week. They’re having a really bad Python packaging situation at the moment for whatever reason; pipx broke at the same time. If you install through any other mechanism (plain pip, pipx, Nix, etc.) I promise it works fine.

                                                            2. 1

                                                              It seems like the encryption is very basic. Do you use that feature, or do you retain your privacy in other ways? https://jrnl.sh/encryption/

                                                              https://www.nccgroup.trust/us/about-us/newsroom-and-events/blog/2009/july/if-youre-typing-the-letters-a-e-s-into-your-code-youre-doing-it-wrong/

                                                              1. 1

                                                                I’m aware that that’s a feature, but I don’t use it; my hard disk is already encrypted, and if you’re on my disk, that’s probably one the less interesting things.

                                                            1. 4
                                                              Mathematical General Crypto $$$ Commercial

                                                              Ranked according to personal preference. I might have forgotten some. But these (especially the first three and the crypto things) are amongst my personal recommendations.

                                                              1. 2
                                                                Bioinformatics
                                                                1. 1

                                                                  I second this!

                                                                  Also any exercise dealing with genomics is a good practice! Lets you explore a completely new world of data structures and algorithms.

                                                              1. 4

                                                                I’ve built my computer literally yesterday, after ~10 years.

                                                                Specs: AMD Ryzen 3700x, 32 GB RAM, 500 GB NVMe SSD, AMD RX 590 GPU. I’m running Manjaro Linux with i3wm on it.

                                                                1. 1

                                                                  what mobo did you choose for ryzen 3700 ?

                                                                  1. 1

                                                                    I went with Asus TUF X570-plus gaming, because I got a recommendation for it.