I figure in addition to the feedback they received from me (and presumably others) at the time they saw a drop in usage and restored the functional version. But they'll try again.

I'm pretty optimistic that by the time google scholar really goes to shit they'll be good enough to pick up the slack.

DrawboardPDF if you want something more full featured and like to annotate, highlight, bookmark and whatnot, particularly if there's any chance you'll also use a stylus

[1] https://www.zotero.org/download/

It feels a bit dated sometimes, but I'm yet to find anything that comes close.

PDFjs was written in JS from day one, and (as far as I know) was not based on any previous PDF reader.

BTW, I didn't mean they necessarily used the actual Foxit code, but it was a starting point maybe reimplemented in JS.

https://www.mozilla.org/firefox/browsers/

STDU Viewer might also be worth looking into. Default shortcut for jumping back is ctrl+z.

But most importantly.. ALT+'left arrow' allows you to go back before you clicked on the citation! It doesn't work all the time, but usually it does after some left arrows ;)

Also, in Android: you can click on the 'scrolling sign' on the right of the pdf and specify the page, or see the link to 'jump back' to before you clicked on a link!

I hope that will help

Edit: Also, Chrome now defaults to this extension for rendering any PDFs you load.

What are you trying to do? Why is webgl the key here?

I don't even want to imagine having to migrate all annotations and citations to something else when they inevitably pull the plug on it some years down the road.

This makes me nervous. I'm often looking at PDFs that are embedded in a page (either grad school software for commenting on PDFs, or publishers' sites). Is it going to play nicely with those? Is this only for navigating directly to a PDF?

[1] https://www.knowledgegarden.io/

More fundamentally, we need to stop disseminating scholarly work as PDFs, a format primarily designed for print. Plain HTML would be an improvement. Even better than HTML would be an extended variant with scholarly-specific semantic markup and universal, animated, explorable figures. Embedded notebooks would be cool, too, but disseminating data would still be a major challenge. (And I don't just mean storage/transfer; a lot of researchers are reluctant to share source data to the world.)

Can you elaborate where you think Zotero drops the ball?

then is the way you store the pfds. if you want to sync between multiple computers you have to either know how to work with webdav or know how to point zotero at the location where you have your pdfs or (what they most certainly love) pay a lot of money for not so much storage space on their system. that last thing is what i don't like because i just don't trust anyone these days. you get invested in a system, build your routine around it only for them to shut it down, sell it watever and then puff you have to start over.

people keep calling zotero foss but if they were truly foss they would have a much more transparent way for people to roll their own selfhosted zotero server. instead, what they have is a dump of an old version, with next to zero documentation and a bunch of stubborn people that have managed to get something working but not quite.

I get that they are trying to make money but I am sure they could do that and be more transparent.

The other thing is the reliance on so many plugins. While zotero itself may last a while, who can say anything about the many devs of the many plugins that you end up relying on in order to make zotero bow to your routine? I like zotfile and a few others, but how long are they going to last? Also, reinstalling my system is a huge pain to get back to my routine because I have to remember all the settings for each and every plugin I install. They should come up with a way to save all these settings and restore them, and no don't do it through another plugin!

I realized that it helped me to get rid of exactly the pain with fresh installs that you mention. I realized that the two plugins give me most of the functionality that I want.

https://habr.com/ru/articles/443798/

My point is that it is possible to achieve in principle and in practice, albeit that might be practiced as often as one would like to see.

-------

[0] See SingleFile by gildas at https://addons.mozilla.org/en-US/firefox/addon/single-file/: “Save an entire web page—including images and styling—as a single HTML file.”

For example, I once backed up a page using it, and while it got all the content, it did not grab the JavaScript necessary for the images to display correctly.

Re. self-contained HTML (and slightly off-topic), look at TiddlyWiki, which contains data/code/layout all in one interactive, local or hosted HTML. Extensibility, plugins, and community of contributors are some key highlights, among others.

[1] https://www.tiddlywiki.com

I’d much rather have something akin to the CHM files where everything I need is in one file, easy to analyze, and has good readers.

Feelings and promises are each one thing. Reality is another. PDF doesn't even look "the same" today. I have serious questions about how often folks who think that PDF is reliably consistent from system to system step outside their bubble and just how diverse their setups are that they're testing on.

> is HTML the same way?

Well the status-quo for copy-and-paste in HTML isn't dogshit, it's comparatively trivial to find and use tools that can thoroughly and exhaustively search your collection (or even write your own), and HTML is a dead simple plain-text format that if worst comes to worst you can read with your eyes (unlike needing to run a bunch of inscrutable code from a PostScript subset through an interpreter before you can do anything with it). So, no, I wouldn't call them the same.

MacOS and iPad: DevonThink paid app with sync via P2P, WebDAV or cloud services.

Optional local mirror/sync of web pages and PDFs, with full text search.

I like the experience of reading in Muse.app on the iPad. It's a nested whiteboarding thing, but also can act as a PDF reader. (It'll let you pull out chunks of the PDF and put it on your canvas with a link back into your document, if that fits your flow.) I often read on my phone, so this is not an option for me.

Apple Notes and Muse slow down with a lot of ink. For taking a page full of notes I'm using Notability.

I've heard good things about GoodReader, but haven't played with it in years.

It seems to work in MacOS and iOS; an iCloud account is probably required.

https://apps.apple.com/us/app/pdf-expert-editor-reader/id743...

The Elsevier account integration is disgusting though, and I hate the idea of using all Elsevier product.

Other than that the commenting and note reader UI was pretty good. And overall UI/UX felt more modern than Zotero, also free (as in beer) cloud backup.

Today I had to do some literature review, and I reinstalled Zotero 7beta because I am not happy with the removed functionality from Mendeley.

On the paper organization side, I would also like to find out a better way of doing it. What helps me a lot, from a more methodological perspective, is to categorize books according to time period, school of thoughts, or perspective.

Also, is the data store encrypted at rest even when the app is actively being used?

The data is all local, so there's no need for encryption yet. But when we implement sync it'll be end to end encrypted.

    folders:
        - for every literature search, create a folder with date and name
            - e.g. 2024-03-21_Quantum_Entanglement
            - use CTRL-SHIFT-DRAG to drop files into Zotero as Links, see [#77](https://github.com/zotero/zotero/issues/77)
            - You _can_ organize in Zotero, but you don't have to. Files can be linked
            to multiple Zotero folders (simply copy library entries in Zotero)
            - sync literature folder and zotero database with nextcloud to somewhere, for backup
    zotero:
        - disable sync
        - set “Base directory” (Preferences > Advanced > Files and Folders) to local literature folder
        - set PDF View to “System default” (Preferences > General > “Open PDFs using..”)
        - Enable recursive quick search in folders: go to Preferences > Advanced > Config Editor, search for `recursiveCollections`, double click (set to True)
        - use CTRL-Shift-C to copy bibliography to clipboard
        - Dark Theme:
            - https://github.com/Rosmaninho/Zotero-Dark-Theme
            - Go to `%AppData%\Zotero\Zotero\Profiles\` (`XXXXXXXX.default`)
            - Create `chrome` folder
            - Place the `userChrome.css`
            - Start Zotero
        - Add-Ons:
            - zotero-pdfkit
                - https://github.com/sharpevo/zotero-pdfkit/
                - allows to modify/select a “default” PDF attachment to be opened
            - ZoteroDuplicatesMerger
                - https://github.com/frangoud/ZoteroDuplicatesMerger
                - easier merging of duplicates
            - zotero-folder-import
                - https://github.com/retorquere/zotero-folder-import
                - bulk import PDFs from a folder
            - zotero-tag
                - https://github.com/windingwind/zotero-tag
                - allows to add stars to items (Num Key `1`, `2`, `3` etc.)
    - PDF Tools:
        - qpdf
            - removing passwords, unlocking PDFs, conversion
            - install in WSL with `apt-get install qpdf`
            - remove password with `qpdf --decrypt --password="" input.pdf output.pdf`
        - `SumatraPDF`
            - _Really_ fast Viewing of PDFs and adding annotations (highlight, comment etc.)
            - Highlight Text: `A`, Save to file: `CTRL+SHIFT+S`
            - it is much faster than Adobe Acrobat
        - [pdfplumber](https://github.com/jsvine/pdfplumber)
            - Awesome python package to extract tables from PDFs into data pipelines. Use with Jupyter Lab.
        - [PDF X-Change viewer](https://www.tracker-software.com/product/pdf-xchange-editor), `choco install pdfxchangeviewer`
            - for manual OCR of pages/PDFs

> LaTex math in Zotero note is no longer a dream. The `zotero-better-notes` addon now supports this feature!

[1]: https://github.com/windingwind/zotero-better-notes

[1] https://github.com/vedang/pdf-tools

[2] https://github.com/jkitchin/org-ref

I have a google docs for each research project and thus I can share them with my collaborators. Each person has their own section within the doc so we can also easily share information with each other!

i've variously seen apps call this "Extra Dark," "Midnight mode," "OLED dark," "Pure Black", ...

So it's a closed ecosystem for now ... pass.

I did try all the devices you listed above, even had my department pay serious money, and ended up barely using them for all those reasons. I am a mathematician, I am clumsy and I want to focus on my problem-solving; I want to think, and babysitting devices and tools is not what I want to spend my brainspace on.

... is what I get told all the time.

[1] https://www.brother-usa.com/supplies/ink-and-toner#sort=rele...

[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3987331/

https://www.scholars.io

Let you import and read PDF directly, annotate, comment and share with people.

Unless you need to scroll left and right on your phone instead of absorbing

* Summarisation

* Succinctly placing the research in context of the broader field

* Highlighting limitations or flaws in research methods, etc.

* An outline view to summarise each paragraph/section and then drill down into the ones you actually want to read in more detail

* Rephrasing into plain English. A lot of academics enjoy sounding clever and usling long words so it'd be nice to be able to switch off "ego mode" and just read stuff in plain English instead of having to wade through their word-soup.

With more effort maybe Google could create a PDF reader that is actually innovative.

"Sounding smarter through obscurity"

Maybe this just needs a script? I just paid $100 for EndNote 21 yesterday and don’t think these needs justify that cost.

[1]https://www.zotero.org/