6 ms·

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 wis

by jinay 3y ago

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.

mixedmath 3y ago
What does AI assisted reading mean to you?
- jinay 3y ago
  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.
gillesjacobs 3y ago
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.
- felipefar 3y ago
  What do you like about organization in Mendeley?
  - gillesjacobs 3y ago
    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.
- malshe 3y ago
  I use zotfile extension to automatically rename files in Zotero
jdeaton 3y ago
Paperpile is fantastic and you can make a shared folder with your lab/team.
felipefar 3y ago
I was also unhappy with how reference managers handle annotations. So I rolled my own app (https://getcahier.com 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.
- ukuina 3y ago
  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 3y ago
    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.
- oldandtired 3y ago
  Doesn't support Linux though or any of the unixes. Looks good though.
  - felipefar 3y ago
    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.
pks016 3y ago
I use Zotero with a bunch of useful Addons. Currently, scite is best available tool for research papers (at least in my field).
- jinay 3y ago
  Scite seems to apply to all fields, any reason why it's particularly good in yours?
Helmut10001 3y ago
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
- 3y ago
hahajk 3y ago
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 3y ago
  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.
magical_spell 3y ago
pdf-tools [1] + org-ref [2] in Emacs. [1] https://github.com/vedang/pdf-tools https://github.com/vedang/pdf-tools [2] https://github.com/jkitchin/org-ref https://github.com/jkitchin/org-ref
Labo333 3y ago
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!
cevi 3y ago
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 3y ago
  That seems really useful, thank you!

by jinay 3y ago

mixedmath 3y ago

What does AI assisted reading mean to you?

jinay 3y ago
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.

gillesjacobs 3y ago

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.

felipefar 3y ago
What do you like about organization in Mendeley?
- gillesjacobs 3y ago
  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.
malshe 3y ago
I use zotfile extension to automatically rename files in Zotero

jdeaton 3y ago

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

felipefar 3y ago

I was also unhappy with how reference managers handle annotations. So I rolled my own app (https://getcahier.com 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.

ukuina 3y ago
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 3y ago
  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.
oldandtired 3y ago
Doesn't support Linux though or any of the unixes. Looks good though.
- felipefar 3y ago
  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.

pks016 3y ago

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

jinay 3y ago
Scite seems to apply to all fields, any reason why it's particularly good in yours?

Helmut10001 3y ago

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

3y ago

hahajk 3y ago

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 3y ago
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.

magical_spell 3y ago

pdf-tools [1] + org-ref [2] in Emacs. [1] https://github.com/vedang/pdf-tools https://github.com/vedang/pdf-tools [2] https://github.com/jkitchin/org-ref https://github.com/jkitchin/org-ref

Labo333 3y ago

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!

cevi 3y ago

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 3y ago
That seems really useful, thank you!