[jinay]

Does anyone have a research paper reading tool they're happy with? Zotero is what meets most of my needs but I wish I could organize the papers faster and I wish the annotation tools were better. AI-assisted reading is a plus too.

[felipefar]

I was also unhappy with how reference managers handle annotations. So I rolled my own app (https://getcahier.com), with highlight management integrated in the application. This enables me to extract highlights according to topics, organize them in notes using document elements (like collapsible notes and outlines) and use them to plan more complex arguments. This makes it much easier to read actively.

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.

[oldandtired]

Doesn't support Linux though or any of the unixes. Looks good though.

[felipefar]

Thank you for your interest! I've received that request more than I thought I would. It's high on the priority list now, and will arrive soon.

[ukuina]

Cahier looks great! Any plans to add backup/sync?

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

[felipefar]

Thanks! I'm considering that. We might first implement P2P or external services (dropbox, iCloud) sync, but we'll see.

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.

[cevi]

evince recently added some features that I now find it hard to live without. The biggest is that if I mouseover an internal link in a pdf, it shows a little preview of where that link would take me - so if I'm reading a long document and the author says "by Theorem 3.3 it holds..." and if the pdf is recent enough for "Theorem 3.3" to be an internal link, then I can mouseover to remind myself of the statement of Theorem 3.3!

[jinay]

That seems really useful, thank you!

[Helmut10001]

I use a combination of Zotero, Locally Linked PDFs/Folder Structure, and SumatraPDFs (Comments etc.):

    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

[gerroo]

Do you know if there's a way to write latex comments in Zotero / Mendeley? It's something I've been looking for.

[Helmut10001]

Did you check the `zotero-better-notes`? [1]

> 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

[gerroo]

Thanks for that :)

[hahajk]

Readwise Reader has a nice pdf reader with highlighting, notes, and an AI reader tool. I organize sources using tags. It's very new and in active development. Academic research is not it's main focus, though, so it probably won't add mindblowing academic tools. (like citation support/ backlinks. although it does have internet backlinks that tell you want articles link to the one you're reading)

[1123581321]

Readwise Reader is a poor PDF reader, unfortunately. Where it shines is making readable text documents out of PDFs, so it depends on the type that you’re reading.

[Labo333]

Nothing quite beats a simple google docs file where I can take notes and put links to sci-hub. Very often, legal download links expire after some time or they force the browser to download the pdf.

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!

[mixedmath]

What does AI assisted reading mean to you?

[jinay]

Those "chat with a PDF" apps get me halfway there, but I'm more imagining something that can explain certain terms in the context of the paper, or automatically dive into the citations and pull explanations from them too.

[jdeaton]

Paperpile is fantastic and you can make a shared folder with your lab/team.

[pks016]

I use Zotero with a bunch of useful Addons. Currently, scite is best available tool for research papers (at least in my field).

[jinay]

Scite seems to apply to all fields, any reason why it's particularly good in yours?

[magical_spell]

pdf-tools [1] + org-ref [2] in Emacs.

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

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

[gillesjacobs]

Mendeley beat Zotero for me with automatic pdf renaming, organising and its highlight and note taking tools in the reader.

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

[malshe]

I use zotfile extension to automatically rename files in Zotero

[felipefar]

What do you like about organization in Mendeley?

[gillesjacobs]

Ever since the big UX app overhaul there is not much to like regarding functionality. They removed the pdf renaming and some other major automated file mgmt features from mendeley.

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.