I installed before I even got to the end of the feature list. I like it a lot, though it could use some improvements - I miss 2 page display, for example.
While the keyboard control interface is great the absence of menu commands is not. It's weird to me that there's no way to bring up a help display from within the program (there's one there when you first open, but it vanishes as soon as you open something); I had to go to the website and move to the documentation page to see that I was doing.
Still, it has so many good features built in that are optimized for research that it's worth the inconvenience.
I've been working on having my notes better integrated with the content I read. I try to gather references to where an idea is developed/contradicted in the literature, or just collect good ideas.
Cahier (https://getcahier.com), the software I'm developing, supports creating cards with references to passages in the PDFs read.
It's exciting to see the developments that are being made in this area in the past few years.
Cahier looks like exactly what I’ve been hoping for for a long time. People have been taking “knowledge management” seriously for a few years now and we have a number of great tools like Obsidian, Zotero, Anki, and their brethren. But there’s still no real good solution to properly highlight and annotate documents, then link those outside their originating document into the broader context of one’s notes. Instead you end up with multiple silos—a Zotero full of papers, an Obsidian full of notes etc. This strikes me as a definite step in the right direction—thinking about knowledge management as an integrated process, with a workflow right through from reading, to taking notes, to organising those notes, to actively employing them to generate new insights and effectively write.
(I guess my only concern is around potentially reinventing the wheel when it comes to some of these areas. E.g. do you plan to integrate every feature from Zotero, like the web-integrated grabber? That sounds like a prodigious amount of work, but without it it’s hard to fully supplant Zotero as a reference management solution. I’m curious as to your roadmap for this and what you see as the ultimate feature set and user workflow.)
This looks really good, thanks for sharing. Like other commenters, I use Zotero and will probably stick to that for the near future. The main feature for me in Zotero is sync'ing across devices. I usually read and annotate papers on iPad, and love that my highlights and notes are synced for when I write and need to reference them on either my MacBook or Windows desktop.
Your note-taking solution seems far superior though. Sometimes I wish we could smash together different software into just the right thing for us.
Could you expand on what you see as exciting developments? I’ll have to check out the op post link as well as yours and others in the thread.
It’s been a few years since I seriously looked at options for my personal use, but I remember being quite disappointed in the options I found. Zotero and org-noter seemed two of the best (though in completely different ways) pieces of software I could find regarding reading or organizing pdfs. I trialed OneNote for a year and liked it in the moment, but zero support for navigation or discovery or review of information make it untenable for building a knowledge base or doing literature review.
I imagine that software which makes reading and connecting document information (in any form: pdf, html, video or other) could be so much better than what I use daily.
That looks very interesting. An essential feature for me is data, including my notes and annotations, that will remain usable in the long run - many decades into the future.
Otherwise, my work of today is lost. What happens if you stop making Cahier someday or if I need to move to another system?
For reference management I'm finally sticking with Zotero after maybe 15 years of trying it. With version 7 beta it's finally becoming really good for my use-cases.
I use this all the time. It's a nice app. Although some of the features such as jumping to citations are available in Google Scholar extension for Chrome. I just love the idea of vimifying my apps. Before Sioyek, I used Karabiner to set j/k/etc. in macOS Preview so I could navigate using vim keys, but that was a tedious process and didn't have many features that Sioyek offers. Also, I use a solarized background color for PDFs to avoid eye strain, and the app supports night mode even for the graphs in PDFs!
Some gripes with this app:
- There's an extension that lets you view PDFs in two columns (panels) side by side. But that literally changes the actual PDF files!
- Plugins are generally challenging to install. I found a workaround and reported it, but IDK if the author took that feedback to improve the app.
- To my knowledge, the app stores its configs in the Applications directory of the app. It'd be nicer to have them in ~/.config.
- The feature to quickly open files in a directory doesn't work for cloud drives (including iCloud).
I took a bit more collaborative approach to reading and discussing research papers (https://www.scholars.io or https://app.scholars.io) and allow people to annotate, comment and collaborate on research.
As a simple workaround for the "flip between two pages" feature that is so easy in dead tree but harder on computers, I usually just open the pdf twice, if the software allows two running copies, or if the software is too clever, I just copy the pdf into a second copy and open that. I can then alt-tab between them and scroll to different parts.
On the phone, I can use Acrobat Reader and Koreader at the same time.
Tangentially related. does anyone know a good pdf reader with LLM based search integrated? Suppose I want search for "cities in USA", in the document, it should show all occurences new york, los angeles and chicago, for example.
I really liked Sioyek as a more fully-featured Zathura, but two features kept me from using it as my primary PDF reader:
1. Can't open multiple PDFs at the same time: Trying to open a second PDF with it while it's already open with some PDF crashes both instances.
2. Annotations are stored in a separate document rather than the PDF itself.
Other users have noted both of these before. I didn't find an easy fix to 1, and a partial solution to 2 uses an extension, but IIRC it still requires manually running a command to transfer annotations to the PDF document itself.
Agreed on the multiple PDFs (I think that's a WIP), but I'm actually in favor of annotations stored in a separate document rather than embedded in the PDF. Ideally it would be nice to have both options which Zotero and your mentioned extension offer, but I'd prefer to have annotations separate so you can access a 'clean' copy of the PDF to e.g. share with others. Additionally, each PDF viewer that supports 'annotations' currently supports them in its own unique way and programs usually can't distinguish highlights/notes made by other programs from the original source. However, Zotero and a few other readers are starting to use Web Annotation Data Model (https://www.w3.org/TR/annotation-model/) as a universal annotation storage mechanism, which I'm hoping will eventually allow you to create some highlights/notes in Sioyek, view and edit them in KOReader on an e-reader, then send an annotations file to a colleague who uses Zotero or Obsidian/PMK and has their own separate copy of that PDF (something I'm working on but very early on). https://hypothes.is operates a bit like this.
For the latest version (2.0.0): There is supposed to be a setting for (1), but the note in the supplied settings file seems to be misleading. I find that if I set `should_launch_new_instance` to 1, then I can have multiple PDFs open in Sioyek simultaneously, but only if I open the PDFs after the first from the termiinal; opening them from within Sioyek or from dmenu replaces the PDF that’s already open. But I never got any crashes. I use dwm on Debian.
Sioyek developer here. You absolutely should be able to open multiple PDFs (e.g. using the new-window command are passing the --new-window command line option). If you are experiencing crashes please open a github issue.
My favorite feature from this program that doesn't exist in any other PDF reader (AFAIK) is visual mark mode, where it highlight each line you read. Very good to reduce eye strain
Great tool! A feature suggestion: a common complaint about PDFs compiled from e.g. LaTeX is that text elements like "fi" in words such as "profile" cannot be correctly copied due to ligature encoding (e.g. try copying from the title in [1]: "profile" becomes "prole" and "identifiers" becomes "identiers"; also see discussion at [2]). An option to automatically fix this within the viewer could be a desirable feature — though admittedly I haven't thought this through and I'm not sure how feasible it is to implement such a feature at the viewer level.
Is there something like this for iPad? Reading research articles is a painful process having to flip back and forth between text, figures and references all the time
I use GoodReader. I'm open to trying something else, but it has folders, bookmarks, annotations, the basics. It lacks all of the fancy stuff in the linked program, though.
PDF reading is the main use I have for a 13 iPad, and I do enough of it that it justifies the device.
Very nice. It could only be made better by supporting more formats. Like mobi, fb2 and DJVU. I miss Sumatra when using a Mac as it could open all of these beautifully on Windows. Perhaps Sioyek could make a great replacement if coupled with a library like Pandoc.
Years ago during grad school, I used a tool called docear, which can manage papers and had a mind map to documents our ideas. It was a fantastic tool far beyond the time. I still have not found an elegant knowledge management tool like that one
I want an easier way to switch between my blue green and yellow high lighters when reading a pdf for school. Also, how about a menu button that exports highlighted selections into a markdown file?
[+] [-] anigbrowl|1 year ago|reply
While the keyboard control interface is great the absence of menu commands is not. It's weird to me that there's no way to bring up a help display from within the program (there's one there when you first open, but it vanishes as soon as you open something); I had to go to the website and move to the documentation page to see that I was doing.
Still, it has so many good features built in that are optimized for research that it's worth the inconvenience.
[+] [-] hexomancer|1 year ago|reply
[+] [-] Levitating|1 year ago|reply
[+] [-] felipefar|1 year ago|reply
Cahier (https://getcahier.com), the software I'm developing, supports creating cards with references to passages in the PDFs read.
It's exciting to see the developments that are being made in this area in the past few years.
[+] [-] CiceroCiceronis|1 year ago|reply
(I guess my only concern is around potentially reinventing the wheel when it comes to some of these areas. E.g. do you plan to integrate every feature from Zotero, like the web-integrated grabber? That sounds like a prodigious amount of work, but without it it’s hard to fully supplant Zotero as a reference management solution. I’m curious as to your roadmap for this and what you see as the ultimate feature set and user workflow.)
[+] [-] halgir|1 year ago|reply
Your note-taking solution seems far superior though. Sometimes I wish we could smash together different software into just the right thing for us.
[+] [-] angleofrepose|1 year ago|reply
It’s been a few years since I seriously looked at options for my personal use, but I remember being quite disappointed in the options I found. Zotero and org-noter seemed two of the best (though in completely different ways) pieces of software I could find regarding reading or organizing pdfs. I trialed OneNote for a year and liked it in the moment, but zero support for navigation or discovery or review of information make it untenable for building a knowledge base or doing literature review.
I imagine that software which makes reading and connecting document information (in any form: pdf, html, video or other) could be so much better than what I use daily.
[+] [-] unknown|1 year ago|reply
[deleted]
[+] [-] tudurom|1 year ago|reply
[+] [-] wolverine876|1 year ago|reply
Otherwise, my work of today is lost. What happens if you stop making Cahier someday or if I need to move to another system?
[+] [-] burgerrito|1 year ago|reply
[+] [-] rossant|1 year ago|reply
For reference management I'm finally sticking with Zotero after maybe 15 years of trying it. With version 7 beta it's finally becoming really good for my use-cases.
[+] [-] behnamoh|1 year ago|reply
Some gripes with this app:
- There's an extension that lets you view PDFs in two columns (panels) side by side. But that literally changes the actual PDF files!
- Plugins are generally challenging to install. I found a workaround and reported it, but IDK if the author took that feedback to improve the app.
- To my knowledge, the app stores its configs in the Applications directory of the app. It'd be nicer to have them in ~/.config.
- The feature to quickly open files in a directory doesn't work for cloud drives (including iCloud).
[+] [-] pyromaker|1 year ago|reply
[+] [-] ufo|1 year ago|reply
[+] [-] exe34|1 year ago|reply
On the phone, I can use Acrobat Reader and Koreader at the same time.
[+] [-] drwu|1 year ago|reply
[+] [-] throwaway425933|1 year ago|reply
[+] [-] indit|1 year ago|reply
[+] [-] vinceroni|1 year ago|reply
[+] [-] atkirtland|1 year ago|reply
Other users have noted both of these before. I didn't find an easy fix to 1, and a partial solution to 2 uses an extension, but IIRC it still requires manually running a command to transfer annotations to the PDF document itself.
[+] [-] ryanwwest|1 year ago|reply
[+] [-] leephillips|1 year ago|reply
I consider (2) desirable.
[+] [-] hexomancer|1 year ago|reply
[+] [-] burgerrito|1 year ago|reply
My favorite feature from this program that doesn't exist in any other PDF reader (AFAIK) is visual mark mode, where it highlight each line you read. Very good to reduce eye strain
[+] [-] anthk|1 year ago|reply
[+] [-] aragonite|1 year ago|reply
[1] https://www.unicode.org/L2/L2022/22230-math-profile.pdf
[2] https://tex.stackexchange.com/questions/33476/why-cant-fi-be...
[+] [-] pazimzadeh|1 year ago|reply
[+] [-] 0x38B|1 year ago|reply
It’s definitely worth trying.
[+] [-] samatman|1 year ago|reply
PDF reading is the main use I have for a 13 iPad, and I do enough of it that it justifies the device.
[+] [-] sva_|1 year ago|reply
[+] [-] vzaliva|1 year ago|reply
[+] [-] ykonstant|1 year ago|reply
[+] [-] k310|1 year ago|reply
[+] [-] qwerty456127|1 year ago|reply
[+] [-] wanderingmind|1 year ago|reply
[+] [-] thy77|1 year ago|reply
[+] [-] nailer|1 year ago|reply
Essentially, as if they had never been written in PDF in the first place. Does anyone know if such a thing exists?
[+] [-] sebmellen|1 year ago|reply
[+] [-] james_chu|1 year ago|reply
[+] [-] kranner|1 year ago|reply