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...
In Word, alt-1 click reference, alt-2.
Its done. Reference inserted. Bibliography updated. Sweet.
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.
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.
- 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.
(Disclosure: Zotero dev)
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.
> 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.
No, we don't expose your data to anyone else. (And tools that try to do that usually just end up filling people's libraries with junk data.)
You should sync Zotero if you want to 1) access your library on other devices, 2) collaborate with others, and/or 3) have a real-time backup of your Zotero data.
Zotero is great! :)
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_beDLtsTm....
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.
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.
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.
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.
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...
The reason this happens is Elsevier's business model. And this business model both really wrecked Mendeley and, I believe, contributes to medical misinformation being more dominant in the world.
And I don't think medical misinfo has much to do with Elsevier or academia. It's human nature, and the quality and degree of evidence-basedness of official communications doesn't really help.
Also, the words "misinformation" and "fact check" make my skin crawl.
If your conclusion is that the plebs is so dumb because they listen to Joe Rogan instead of The Science(TM), I think you're just digging in deeper.
Also, during the pandemic, many blue check Twitter accounts said it's a pity that so many conspiracy theorists and fake news believers are reading papers and playing around with data. They should just receive The Science, spoon-fed, and accept it, and too much thinking and reading hurts them. In other words, think about what you wish for. When other people are given access to data, they may reach different conclusions than the approved respectable media expert consensus.
Not sure what that means? Is he hiding true science and research?
The most informative papers are often behind a paywall, so the non-paywalled papers are biased towards these other less-informative and even wrong papers.
If someone should point to paper X, in order to correct a mistaken belief discussed in a public form (like HN), and that paper X cost $50 to read, many fewer people will read it to examine the validity of the paper in the first place - even if were correct.
While if someone points to paper Y, which supports that belief due to subtly wrong assumptions, but that paper is free to read, then many more people are likely to look at it. And without the training or experience to identify the wrong assumptions.
None of this requires our "Joe Rogan" to hide true science and research - paywalls already do that.
For him it's probably sufficient to just use a heavily-biased selection of it and/or present a heavily-distorted version of its results. (As others in the thread have pointed out, the hiding is done efficiently enough by others, i.e. the heavily-paywalled scientific journals.)
I think that was much more caused by media trying to prime people with some ridiculous stories that at least some refused to believe. A simple but honest approach is preferred to what we read in media otherwise.
We still have sci-hub at least...
What does that have to do with Open Source?
> Also APCs skew who can publish 'well'. The APCs for some top Cell and SpringerNature journals are about ten thousand fucking dollars.
What are APCs? (Are they perhaps what relates to Open Source here?)
> Great that the public can access it but that's money that either doesn't go to research or has to come out of taxpayer funded grants and straight into the pockets of publishers with huge margins. OA has also spawned a massive predatory journal market.
But even ten thousand fucking dollars sounds a lot less than what those publishers are making now, so isn't it still much better?
APCs are article processing charges. They are the fees the author (or sometimes the institution, if they have negotiated a blanket deal for all of their researchers) pay the publisher in exchange for the article being made open access.
> But even ten thousand fucking dollars sounds a lot less than what those publishers are making now, so isn't it still much better?
Publishers wouldn't be transitioning so many journal to Open Access if it was hurting their bottom line, and the for-profit academic publishing industry is about as profitable as they come with margins approaching 50%. They can do it under the guise of a principled stand. But it can create some perverse incentives. Also, previously they made money from subscription fees, so the bargaining power of whole university systems would negotiate rates. Now it for the most part falls to individual researchers, who don't have that economy of scale type bargaining power, which removes that check on inflation. A few Uni systems have cut similar deals to cover APCs for their faculty as I mentioned earlier, but it isn't yet the norm. /rant
Holy shit. If all this is for "peer review", it's time to scrap how they get that and develop a whole new peer review system.
(Are the Swedish Academy's science committees so superficial that they just compare citation numbers for awarding Nobel prizes? If not, what system do they use -- and why aren't they open sourcing it?)
There is a model with journals like PeerJ with relatively cheap APCs and a deal where you could sign up for a life membership and publish there indefinitely (but I think coauthors would need to as well). They also only publish based on scientific merit and aren't selective on 'impact', which is good. However, that means they aren't seen as prestigious, so you can't exactly build a career and get promotions going that route.
RE: peer review, in part bc of disruptions due to COVID journal editors have been having a harder time getting people to volunteer to peer review. There has been a lot of talk about moving to a model where reviewers get paid, but again that seems like it would set up some perverse incentives.
RE: Nobel, I don't think it is about citations, pretty sure the judge the impact of a particular body of work/discovery/contribution, qualitatively.
Yeah, I pretty much knew (or at least assumed) that. My question was more a half-facetious way of saying academia in general should also do it that way in stead of continuing the current stupidly simplistic quest for journal citation counts.
Sure, I know nobody can afford to invest the same kind of work for every one of the millions of papers produced each year as the Nobel committee does for a few potential laureates. So it would have to be some kind of distributed system, based on the whole international scientific collective... An adaptation of the Slashdot rating system, or something? :-)
And I wholeheartedly second the fact Mendeley is Evil. I got sick of the bugs.
What a massive and disappointing oversight. Otherwise I could've seen it becoming my new research manager.
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
As of a few years ago there is also a Windows app, and you can use it in the browser. https://papersapp.com
My biggest frustration with Zotero is that it has no real support for standards documents.
On the upside, no one with a little bit of academic cred would use Pages.
LaTeX would be nicer but....biologists.
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 :(
Scripts produce figures as PDF files. We aim to have the script produce more-or-less final figures, but sometimes the last 5-10% is easier to do manually.
We don't bother putting them into the manuscript text while editing, and the captions are usually on a separate page, as most of our target journals seem to require. The manuscript gets written in Word + Endnote, with ad-hoc figure reference like See Figure XXX_DOSE_RESPONSE_XXX that get find-replaced at the very end.
This is definitely a local optima (if that!), but works pretty well for us especially since it's a pretty diverse group: some computationally-minded folks might be happier with LaTex, but we've also got 85 year old prof, DoD folks, etc who want track changes and familiarity.
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.
An absolute must have is BetterBibTex (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) 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.