7 ms·

Zotero is, if you're not in the market for a closed source silo like EndNote, the only game left in town. Mendeley went full on Evil, and Papers for Mac is Mac

Zotero is, if you're not in the market for a closed source silo like EndNote, the only game left in town. Mendeley went full on Evil, and Papers for Mac is Mac only, closed source, and missing dozens of functionalities that are absolutely a must have in academic writing and research. An absolute must have is BetterBibTex (https://retorque.re/zotero-better-bibtex/ https://retorque.re/zotero-better-bibtex/), which adds better Citekey management and, my personal highlight, "export on add" functionality. In short, everything I save into a specific folder in my library gets exported as a .bib file right away. That way I can click a button in my browser and have the citation ready in my LaTeX editor, Word, or Obsidian (https://github.com/hans/obsidian-citation-plugin https://github.com/hans/obsidian-citation-plugin) within seconds. The latest beta also adds full Markdown export for Notes. I tend to keep my notes on papers in Zotero, attached to the paper, but export them for filing in Obsidian (which I then feed into MkDocs for our work group's large repo). Unless you need Apple Pages support, which Apple keeps to itself and only sells for mighty moolah to a select few, Zotero can do anything EndNote can do, is Open Source, and with that won't drive your PI up the wall with yet another expense.

WayToDoor 5y ago
> Mendeley went full on Evil Could you explain what happened with mendeley? I've been using it for a while, and didn't notice anything different really.
- carbocation 5y ago
  They locked down the SQLite database so that you couldn't use it with 3rd party tools (such as your own commands, or to export). I am not sure if this got reversed, but at the time it was what triggered me to switch to Zotero. (Still using Zotero, which does everything I need it to.) One thing I like a lot about Zotero is that they charge a subscription once you get over a certain amount of cloud storage, which gives me more confidence that they'll continue to exist in the future.
  - kelsolaar 5y ago
    Yes, the DB was encrypted for no good reason except that locking users. Funnily enough at that point Mendeley could import from Zorero but Zotero could not import anymore. Thanks to Greydon Gilmore and GDB, I was able to get out: https://blog-academic.greydongilmore.com/phd_related/mendeley_decrypt.html https://blog-academic.greydongilmore.com/phd_related/mendele...
    - tonyg 5y ago
      Greydon's page is based on my original article: https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db.
- medimikka 5y ago
  Mendeley joined the Elsevier "Family." Elsevier is one of the big three making massive amounts of money by selling content they receive for free, paid for by the tax payer or non-profits. I strongly believe, that this has greatly contributed to the "Joe Roganization" of the pandemic, hiding true science and research, often created under the auspices of governmental research trusts, behind a paywall. Anyone not in academia (where Elsevier charges hundreds of thousands to institutions to give their researchers access to their own papers) is more or less SOL and gets their data from Joe Rogan. In that vain, Elsevier has a tight control on the app now. Zotero has the ability to find the open access version of a paper, Elsevier will always link to the paywalled version on its own servers. Zotero has (and Mendeley had) the ability to export libraries, and with that data, Elsevier removed that when they took over Mendeley development. And, worst of all, Zotero can run standalone, Mendeley now requires an Elsevier ID login. The company actively analyzes your reading data and advertises other Elsevier properties based on your interests and reading habits. This is academia. It should be open and accessible. Elsevier is doing everything they can to change that. And Mendeley is one weapon in their arsenal.
  - bonoboTP 5y ago
    The Joe Rogan part makes no sense to me. Only a fraction of the listeners of the podcast would otherwise go out of their way to read primary science journal articles. Reading those is a skill and requires background knowledge to be able to read between the lines, shared context between experts etc. Scientific articles aren't written for a lay audience. Also, sci-hub exists.
    - medimikka 5y ago
      > Also, sci-hub exists. Try adding one of those papers to Mendeley. Or, for that matter, get it by request from the author. Legal and often fast. Add that. See what Mendeley does with the CiteRef.DOI and CiteRef.URI fields...
      - bonoboTP 5y ago
        Are we talking about Mendeley or the general Elsevier paywalls? Seems like you are complaining about several issues at once: Mendeley's restricted features, Elsevier's paywall (that can be relevant even for non Mendeley users) and JoeRoganization, by which I guess you mean that his guests don't always confirm mainstream expert consensus (The Science).
- bonoboTP 5y ago
  They got bought by Elsevier who I don't trust for a moment and they are pushing some weird social media angles and the whole thing smells of proprietary vendor lock in, walled-garden etc. Zotero is much more hacker-friendly.
- jjoonathan 5y ago
  Hypothetically speaking: going to scihub, pirating an Elsevier paper, and then uploading proof that you had done so to an Elsevier cloud account doesn't strike me as the brightest of moves. Not in the sense that I think you are guaranteed to see consequences, or in the sense that I've actually heard about it actually going sideways, but to my intuition it does seem like the kind of thing that might attract one of those "pay us $10k or we sue you for $10M" letters down the line.
  - solarkraft 5y ago
    Especially from that company.
- dwiel 5y ago
  In addition to the other responses to this question, they also got rid of their browser plugins that let you quickly add arxiv pages/pdfs/etc in one click with automatic metadata detection. Worked from any browser on Android and desktop. I've yet to find anything like it.
- hank_z 5y ago
  Mendeley for iOS system was discontinued and taken off from App Store for “no reason”. Users are forced to use their web version in iOS system.
vondur 5y ago
I believe Pages is free for Mac users. I do agree that Zotero is a an awesome product.
- commoner 5y ago
  I think GP is referring to the ReadCube Papers app, which is actually also available on Windows, mobile, and as a web app: https://www.papersapp.com https://www.papersapp.com However, in light of its monthly subscription pricing, I'll be sticking with Zotero which does everything I need on a desktop computer, and also with Linux support. Zotero being free and open source gives me confidence that my data won't be encrypted in a user-hostile way like Mendeley did to its users after it was acquired by Elsevier.
- medimikka 5y ago
  Yes, Pages is, but the only citation manager integrating with it is EndNote, because Apple keeps the API locked down and expects quite the payment and revenue share to open it up. On the upside, no one with a little bit of academic cred would use Pages.
  - mattkrause 5y ago
    We've started doing the "final assembly" of preprints and other self-formatted things in Pages. Placing Figures is still annoying in Pages, but far, far less than in Word. LaTeX would be nicer but....biologists.
    - medimikka 5y ago
      This is totally leaving the original topic, but how do you work figure and table management? In my "smaller" papers, I have 50+ figures (dose-response curves, antibody prevalence curves, etc.) and 10+ tables. Just referencing them based on a handwritten caption, the thought makes my skin crawl. We've gone full in and do most papers in R Studio directly. R Markdown and R Latex work OK, Zotero is integrated, and for the slower members of the team we offer pandoc conversions of their docx and html. But Pages... it does not seem to be made for anyone doing science :(
turboaspie 5y ago
>Zotero can do anything EndNote can do, is Open Source, and with that won't drive your PI up the wall with yet another expense. My university offers EndNote (plus Web of Science and the Clarivate stack) for free for students and many of them don't use it - they'd rather manually manage the bibliography in their Word documents. The university even ran tutorials to show them how to set it up, add citations, and export the references, thinking maybe the students didn't understand the value of bibliography management software. Nope, even with the tutorials there was almost no uptake. It turns out the problem was EndNote all along. I tried it myself - one of the worst user experiences imaginable, and I could totally understand why even doing references by hand is preferable. Eventually I told some of my own students that I use Zotero and to give it a go even though we're not supposed to endorse other software. Two weeks later most of them were using it. So I'm actually quite confused at the fact that Zotero is offered as a free alternative to EndNote, unless the EndNote that I've used is some weird dated inferior version...
- joppy 5y ago
  The university just needs to set an assignment which needs to be submitted twice: once with citation style A, and again with citation style B. Anyone not using citation management software will quickly start.
  - ildon 5y ago
    The point about academic research is freedom, in every possible meaning. Including not using the right tools for the job. This ensures "natural selection" of the ideas, processes and workflows that actually work.
- medimikka 5y ago
  Did you use EN9 or EN20? I found EndNote to be usable, just not something I'd pay $130 (student/academic version) for.
  - kuhewa 5y ago
    It took me until the update to 20 to realise it, but it was Endnote X9 i.e. 19, not 9
dfraser992 5y ago
I forget why I didn't like Zotero - I am using iLibrarian [0]. It is positioned as a SaaS, but the source is available and you can host it yourself. But I can't speak to how it compares to other software as I am not continually using it. It seems I just like collecting scientific papers rather than actually reading them.... Maybe if I live to 150 will I manage to read them all. [0] https://i-librarian.net/ https://i-librarian.net/ And I wholeheartedly second the fact Mendeley is Evil. I got sick of the bugs.
- solarkraft 5y ago
  Oh damn. It looks extremely close to what I want (It's responsive and the PDF UI might even work on my e-reader), but it doesn't seem to support importing web pages?!?!?!?!?!?!?!?!?!?!?!?!?!?! What a massive and disappointing oversight. Otherwise I could've seen it becoming my new research manager.
  - medimikka 5y ago
    It extracts the metadata, but not the body, yes. Retrieved websites are generally frowned upon in my field (medicine, virology), and that's why I never really needed this. We're pandoc-ing our internal MD files to PDF and attach them to the relevant HTML pages, which makes this somewhat a crutch but circumvents the "9 out of ten reviewers hate websites" problem.
  - dfraser992 5y ago
    I print the webpage to a PDF and store it that way, then fix up the metadata as I see fit. And that is a good feature - make a request on the Github repo and see if the lead developer responds.
cycomanic 5y ago
I use zotero and I really want to like it, but it's not that good. The tagging functionality seems like an afterthought, the bibtex support is only reasonable with betterbibtex and even with it I have issues. For example journal abbreviations don't work consistently, every start up I get told that the betterbibtex styles have changed and I need to restart zotero... File management is also only bearable with zutilo, and I still get issues with sync and somehow some file locations getting messed up. The whole note taking experience is also quite soso. I really wish there was a good bib manager around. I don't want to go into a proprietary silo (ruling out mendeley endnote etc.). Jabref is in many ways better then zotero when one uses bibtex, but unfortunately some parts of the UX are not my thing. The best app I have used was docear, the concept of a Mindmapping app together with a bib manager was great however it is unfortunately not maintened any longer.
- only4here 5y ago
  I agree that there are definitely better alternatives to Zotero.
  - jrochkind1 5y ago
    please tell us what you think they are too!
- theteapot 5y ago
  +1 for Jabref and a bibtex database.
  - jll29 5y ago
    I compared some options in 2005: https://www.coli.uni-saarland.de/projects/irtg/contents/Colloquium/WS-05/barbara1.pdf https://www.coli.uni-saarland.de/projects/irtg/contents/Coll... (Not that much changed, except that CiteULike was sunset.) JabRef is a good option for a simple desktop GUI based program that is cross-platform, but I find myself writing "raw" BibTeX entries in Emacs or Sublime more and more often without any UI tools.
- 5y ago
gww 5y ago
What made you decide to take notes on a paper rather than markup the pdf it's self? I have recently been reorganizing my citations as I transition to bring an independent investigator and I have been debating which method I prefer
markdjacobsen 5y ago
Zotero and Obsidian is a killer combination. If anyone is interested, I have some videos on research tools that include a Zotero->Zotfile/MDNotes->Obsidian workflow: https://www.youtube.com/playlist?list=PLHmevVAAXtu3_beDLtsTmkivMI__2b6P8 https://www.youtube.com/playlist?list=PLHmevVAAXtu3_beDLtsTm....
- VladimirGolovin 5y ago
  >> Zotero and Obsidian is a killer combination. Could you elaborate on this a bit? I currently keep my Zettelkasten in Obsidian and my project journals in Workflowy, and I wonder if there’s a place for Zotero in my workflow.
hyperbovine 5y ago
I thought the same thing until I discovered Paperpile. I highly recommend checking it out. https://paperpile.com https://paperpile.com
deleted 5y ago
[deleted]
kobayashi 5y ago
I do not even want to think of what grad school would have been like without Zotero. A shudder-inducing thought.
japanuspus 5y ago
If the town is "online reference managers," you are probably right, but I would argue that reference managers are one of those areas where you really want something offline: - Offline ensures that you do not suffer an externally caused downtime just before a deadline - Offline ensures that you have a path for keeping your database throughout your research career, and to do system updates when _you_ want to. - Offline ensures that if you leave academia, you will always have access to local copies of the academic papers you have referenced. My favorite offline/local reference manager is `jabRef` [0] which stores all metadata directly in a bibtex-file. The GUI has an excellent pdf-integration, and everything is local and super fast. Case in point: after a decade in industry, I am looking to get back into my academic fief. All the papers I ever read are in my Dropbox, and all I had to do to pick up where I left was download a current version jabRef and point it to my database which it read without any issues. [0]: https://www.jabref.org/ https://www.jabref.org/
- dstillman 5y ago
  Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference manager". We strongly agree with all the reasons you give, which is exactly why we designed Zotero the way we did. (Disclosure: Zotero dev)
  - diarrhea 5y ago
    I use Zotero and sync the attachments to my Nextcloud instance via WebDAV. The database is synced to the Zotero servers, because that's the only option. With a bit of care on initial setup for new machines, it works wonderfully. The real value are the PDFs, some of which are of course really hard to get by. And those are "local" in the sense of "local server", yet available to all clients. There was a forum entry that self-hosting the database is a topic being worked on. That's my number one gripe with Zotero, it just seems weird: if using multiple clients, users have to sync to the Zotero servers, yet the storage space for attachments there is minimal (which is okay; Zotero pricing looks reasonable but of course, own storage via e.g. Nextclodu is much, much cheaper). This basically forces a hybrid solution, with bring-your-own-storage. If all of Zotero's data could be self-hosted, now that would be a streamlined, great experience. Then again, I am anal about my entries' metadata and often correct faulty data found online. Syncing that to Zotero servers is kind of like giving back? I always thought that data might help improve Zotero's own auto-fill functionalities, which I'd like helping with.
periheli0n 5y ago
> Papers for Mac is Mac only As of a few years ago there is also a Windows app, and you can use it in the browser. https://papersapp.com https://papersapp.com
fluidcruft 5y ago
>Zotero can do anything EndNote can do My biggest frustration with Zotero is that it has no real support for standards documents.
lijogdfljk 5y ago
On the technical side, anyone know how their browser extension to save webpages.. works? I'm writing a personal reader / reference tool. More of a knowledge base than a formal reference tool, but i want similar functionality, and so i've been researching ways to locally archive web pages to cite in notes. To save effort, i was trying to reuse existing methods in Reader-like libraries. The best i found so far, i think, is Telegram's library of "Instant View" parsers. A community managed set of scrape instructions basically, XPath and whatnot, that i could write an implementation for and - in theory - support everything Telegram does. This is a fair bit of work though. I debated instead simply saving the whole webpage, but that may require saving the JS and i really don't want to execute JS as part of the citation. Anything i might be missing here? Instant View is the only community managed format for scraping i've seen, i'm surprised this isn't more commonly outsourced to communities for Reader modes and whatnot

WayToDoor 5y ago

> Mendeley went full on Evil Could you explain what happened with mendeley? I've been using it for a while, and didn't notice anything different really.

carbocation 5y ago
They locked down the SQLite database so that you couldn't use it with 3rd party tools (such as your own commands, or to export). I am not sure if this got reversed, but at the time it was what triggered me to switch to Zotero. (Still using Zotero, which does everything I need it to.) One thing I like a lot about Zotero is that they charge a subscription once you get over a certain amount of cloud storage, which gives me more confidence that they'll continue to exist in the future.
- kelsolaar 5y ago
  Yes, the DB was encrypted for no good reason except that locking users. Funnily enough at that point Mendeley could import from Zorero but Zotero could not import anymore. Thanks to Greydon Gilmore and GDB, I was able to get out: https://blog-academic.greydongilmore.com/phd_related/mendeley_decrypt.html https://blog-academic.greydongilmore.com/phd_related/mendele...
  - tonyg 5y ago
    Greydon's page is based on my original article: https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db.
medimikka 5y ago
Mendeley joined the Elsevier "Family." Elsevier is one of the big three making massive amounts of money by selling content they receive for free, paid for by the tax payer or non-profits. I strongly believe, that this has greatly contributed to the "Joe Roganization" of the pandemic, hiding true science and research, often created under the auspices of governmental research trusts, behind a paywall. Anyone not in academia (where Elsevier charges hundreds of thousands to institutions to give their researchers access to their own papers) is more or less SOL and gets their data from Joe Rogan. In that vain, Elsevier has a tight control on the app now. Zotero has the ability to find the open access version of a paper, Elsevier will always link to the paywalled version on its own servers. Zotero has (and Mendeley had) the ability to export libraries, and with that data, Elsevier removed that when they took over Mendeley development. And, worst of all, Zotero can run standalone, Mendeley now requires an Elsevier ID login. The company actively analyzes your reading data and advertises other Elsevier properties based on your interests and reading habits. This is academia. It should be open and accessible. Elsevier is doing everything they can to change that. And Mendeley is one weapon in their arsenal.
- bonoboTP 5y ago
  The Joe Rogan part makes no sense to me. Only a fraction of the listeners of the podcast would otherwise go out of their way to read primary science journal articles. Reading those is a skill and requires background knowledge to be able to read between the lines, shared context between experts etc. Scientific articles aren't written for a lay audience. Also, sci-hub exists.
  - medimikka 5y ago
    > Also, sci-hub exists. Try adding one of those papers to Mendeley. Or, for that matter, get it by request from the author. Legal and often fast. Add that. See what Mendeley does with the CiteRef.DOI and CiteRef.URI fields...
    - bonoboTP 5y ago
      Are we talking about Mendeley or the general Elsevier paywalls? Seems like you are complaining about several issues at once: Mendeley's restricted features, Elsevier's paywall (that can be relevant even for non Mendeley users) and JoeRoganization, by which I guess you mean that his guests don't always confirm mainstream expert consensus (The Science).
bonoboTP 5y ago
They got bought by Elsevier who I don't trust for a moment and they are pushing some weird social media angles and the whole thing smells of proprietary vendor lock in, walled-garden etc. Zotero is much more hacker-friendly.
jjoonathan 5y ago
Hypothetically speaking: going to scihub, pirating an Elsevier paper, and then uploading proof that you had done so to an Elsevier cloud account doesn't strike me as the brightest of moves. Not in the sense that I think you are guaranteed to see consequences, or in the sense that I've actually heard about it actually going sideways, but to my intuition it does seem like the kind of thing that might attract one of those "pay us $10k or we sue you for $10M" letters down the line.
- solarkraft 5y ago
  Especially from that company.
dwiel 5y ago
In addition to the other responses to this question, they also got rid of their browser plugins that let you quickly add arxiv pages/pdfs/etc in one click with automatic metadata detection. Worked from any browser on Android and desktop. I've yet to find anything like it.
hank_z 5y ago
Mendeley for iOS system was discontinued and taken off from App Store for “no reason”. Users are forced to use their web version in iOS system.

vondur 5y ago

I believe Pages is free for Mac users. I do agree that Zotero is a an awesome product.

commoner 5y ago
I think GP is referring to the ReadCube Papers app, which is actually also available on Windows, mobile, and as a web app: https://www.papersapp.com https://www.papersapp.com However, in light of its monthly subscription pricing, I'll be sticking with Zotero which does everything I need on a desktop computer, and also with Linux support. Zotero being free and open source gives me confidence that my data won't be encrypted in a user-hostile way like Mendeley did to its users after it was acquired by Elsevier.
medimikka 5y ago
Yes, Pages is, but the only citation manager integrating with it is EndNote, because Apple keeps the API locked down and expects quite the payment and revenue share to open it up. On the upside, no one with a little bit of academic cred would use Pages.
- mattkrause 5y ago
  We've started doing the "final assembly" of preprints and other self-formatted things in Pages. Placing Figures is still annoying in Pages, but far, far less than in Word. LaTeX would be nicer but....biologists.
  - medimikka 5y ago
    This is totally leaving the original topic, but how do you work figure and table management? In my "smaller" papers, I have 50+ figures (dose-response curves, antibody prevalence curves, etc.) and 10+ tables. Just referencing them based on a handwritten caption, the thought makes my skin crawl. We've gone full in and do most papers in R Studio directly. R Markdown and R Latex work OK, Zotero is integrated, and for the slower members of the team we offer pandoc conversions of their docx and html. But Pages... it does not seem to be made for anyone doing science :(

turboaspie 5y ago

>Zotero can do anything EndNote can do, is Open Source, and with that won't drive your PI up the wall with yet another expense. My university offers EndNote (plus Web of Science and the Clarivate stack) for free for students and many of them don't use it - they'd rather manually manage the bibliography in their Word documents. The university even ran tutorials to show them how to set it up, add citations, and export the references, thinking maybe the students didn't understand the value of bibliography management software. Nope, even with the tutorials there was almost no uptake. It turns out the problem was EndNote all along. I tried it myself - one of the worst user experiences imaginable, and I could totally understand why even doing references by hand is preferable. Eventually I told some of my own students that I use Zotero and to give it a go even though we're not supposed to endorse other software. Two weeks later most of them were using it. So I'm actually quite confused at the fact that Zotero is offered as a free alternative to EndNote, unless the EndNote that I've used is some weird dated inferior version...

joppy 5y ago
The university just needs to set an assignment which needs to be submitted twice: once with citation style A, and again with citation style B. Anyone not using citation management software will quickly start.
- ildon 5y ago
  The point about academic research is freedom, in every possible meaning. Including not using the right tools for the job. This ensures "natural selection" of the ideas, processes and workflows that actually work.
medimikka 5y ago
Did you use EN9 or EN20? I found EndNote to be usable, just not something I'd pay $130 (student/academic version) for.
- kuhewa 5y ago
  It took me until the update to 20 to realise it, but it was Endnote X9 i.e. 19, not 9

dfraser992 5y ago

I forget why I didn't like Zotero - I am using iLibrarian [0]. It is positioned as a SaaS, but the source is available and you can host it yourself. But I can't speak to how it compares to other software as I am not continually using it. It seems I just like collecting scientific papers rather than actually reading them.... Maybe if I live to 150 will I manage to read them all. [0] https://i-librarian.net/ https://i-librarian.net/ And I wholeheartedly second the fact Mendeley is Evil. I got sick of the bugs.

solarkraft 5y ago
Oh damn. It looks extremely close to what I want (It's responsive and the PDF UI might even work on my e-reader), but it doesn't seem to support importing web pages?!?!?!?!?!?!?!?!?!?!?!?!?!?! What a massive and disappointing oversight. Otherwise I could've seen it becoming my new research manager.
- medimikka 5y ago
  It extracts the metadata, but not the body, yes. Retrieved websites are generally frowned upon in my field (medicine, virology), and that's why I never really needed this. We're pandoc-ing our internal MD files to PDF and attach them to the relevant HTML pages, which makes this somewhat a crutch but circumvents the "9 out of ten reviewers hate websites" problem.
- dfraser992 5y ago
  I print the webpage to a PDF and store it that way, then fix up the metadata as I see fit. And that is a good feature - make a request on the Github repo and see if the lead developer responds.

cycomanic 5y ago

I use zotero and I really want to like it, but it's not that good. The tagging functionality seems like an afterthought, the bibtex support is only reasonable with betterbibtex and even with it I have issues. For example journal abbreviations don't work consistently, every start up I get told that the betterbibtex styles have changed and I need to restart zotero... File management is also only bearable with zutilo, and I still get issues with sync and somehow some file locations getting messed up. The whole note taking experience is also quite soso. I really wish there was a good bib manager around. I don't want to go into a proprietary silo (ruling out mendeley endnote etc.). Jabref is in many ways better then zotero when one uses bibtex, but unfortunately some parts of the UX are not my thing. The best app I have used was docear, the concept of a Mindmapping app together with a bib manager was great however it is unfortunately not maintened any longer.

only4here 5y ago
I agree that there are definitely better alternatives to Zotero.
- jrochkind1 5y ago
  please tell us what you think they are too!
theteapot 5y ago
+1 for Jabref and a bibtex database.
- jll29 5y ago
  I compared some options in 2005: https://www.coli.uni-saarland.de/projects/irtg/contents/Colloquium/WS-05/barbara1.pdf https://www.coli.uni-saarland.de/projects/irtg/contents/Coll... (Not that much changed, except that CiteULike was sunset.) JabRef is a good option for a simple desktop GUI based program that is cross-platform, but I find myself writing "raw" BibTeX entries in Emacs or Sublime more and more often without any UI tools.
5y ago

gww 5y ago

What made you decide to take notes on a paper rather than markup the pdf it's self? I have recently been reorganizing my citations as I transition to bring an independent investigator and I have been debating which method I prefer

markdjacobsen 5y ago

Zotero and Obsidian is a killer combination. If anyone is interested, I have some videos on research tools that include a Zotero->Zotfile/MDNotes->Obsidian workflow: https://www.youtube.com/playlist?list=PLHmevVAAXtu3_beDLtsTmkivMI__2b6P8 https://www.youtube.com/playlist?list=PLHmevVAAXtu3_beDLtsTm....

VladimirGolovin 5y ago
>> Zotero and Obsidian is a killer combination. Could you elaborate on this a bit? I currently keep my Zettelkasten in Obsidian and my project journals in Workflowy, and I wonder if there’s a place for Zotero in my workflow.

hyperbovine 5y ago

I thought the same thing until I discovered Paperpile. I highly recommend checking it out. https://paperpile.com https://paperpile.com

deleted 5y ago

[deleted]

kobayashi 5y ago

I do not even want to think of what grad school would have been like without Zotero. A shudder-inducing thought.

japanuspus 5y ago

If the town is "online reference managers," you are probably right, but I would argue that reference managers are one of those areas where you really want something offline: - Offline ensures that you do not suffer an externally caused downtime just before a deadline - Offline ensures that you have a path for keeping your database throughout your research career, and to do system updates when _you_ want to. - Offline ensures that if you leave academia, you will always have access to local copies of the academic papers you have referenced. My favorite offline/local reference manager is `jabRef` [0] which stores all metadata directly in a bibtex-file. The GUI has an excellent pdf-integration, and everything is local and super fast. Case in point: after a decade in industry, I am looking to get back into my academic fief. All the papers I ever read are in my Dropbox, and all I had to do to pick up where I left was download a current version jabRef and point it to my database which it read without any issues. [0]: https://www.jabref.org/ https://www.jabref.org/

dstillman 5y ago
Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference manager". We strongly agree with all the reasons you give, which is exactly why we designed Zotero the way we did. (Disclosure: Zotero dev)
- diarrhea 5y ago
  I use Zotero and sync the attachments to my Nextcloud instance via WebDAV. The database is synced to the Zotero servers, because that's the only option. With a bit of care on initial setup for new machines, it works wonderfully. The real value are the PDFs, some of which are of course really hard to get by. And those are "local" in the sense of "local server", yet available to all clients. There was a forum entry that self-hosting the database is a topic being worked on. That's my number one gripe with Zotero, it just seems weird: if using multiple clients, users have to sync to the Zotero servers, yet the storage space for attachments there is minimal (which is okay; Zotero pricing looks reasonable but of course, own storage via e.g. Nextclodu is much, much cheaper). This basically forces a hybrid solution, with bring-your-own-storage. If all of Zotero's data could be self-hosted, now that would be a streamlined, great experience. Then again, I am anal about my entries' metadata and often correct faulty data found online. Syncing that to Zotero servers is kind of like giving back? I always thought that data might help improve Zotero's own auto-fill functionalities, which I'd like helping with.

periheli0n 5y ago

> Papers for Mac is Mac only As of a few years ago there is also a Windows app, and you can use it in the browser. https://papersapp.com https://papersapp.com

fluidcruft 5y ago

>Zotero can do anything EndNote can do My biggest frustration with Zotero is that it has no real support for standards documents.

lijogdfljk 5y ago

On the technical side, anyone know how their browser extension to save webpages.. works? I'm writing a personal reader / reference tool. More of a knowledge base than a formal reference tool, but i want similar functionality, and so i've been researching ways to locally archive web pages to cite in notes. To save effort, i was trying to reuse existing methods in Reader-like libraries. The best i found so far, i think, is Telegram's library of "Instant View" parsers. A community managed set of scrape instructions basically, XPath and whatnot, that i could write an implementation for and - in theory - support everything Telegram does. This is a fair bit of work though. I debated instead simply saving the whole webpage, but that may require saving the JS and i really don't want to execute JS as part of the citation. Anything i might be missing here? Instant View is the only community managed format for scraping i've seen, i'm surprised this isn't more commonly outsourced to communities for Reader modes and whatnot