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Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

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Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#91

Post by gww »

medimikka wrote: post #35

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/ ), which adds better Citekey management and, my perso…

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

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#92

Post by leetrout »

Tangentially I made a Discord server called Awesome Knowledge Management https://discord.gg/XPNeDSQE2j

Inspired by the "who wants to collaborate" post this weekend https://news.ycombinator.com/item?id=29759115

If the folks interested in Zotero and similar products would like to share their experience and also chat about any other similar knowledge management tooling please come join us!

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#93

Post by hank_z »

WayToDoor wrote: post #46
medimikka wrote: post #35

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/ ), which adds better Citekey management and, my perso…

> 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.

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.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#94

Post by jll29 »

theteapot wrote: post #74
cycomanic wrote: post #66

Earlier quoted context omitted.

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, a…

+1 for Jabref and a bibtex database.

I compared some options in 2005: 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.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#95

Post by krull10 »

temp8964 wrote: post #52
kergonath wrote: post #28

Earlier quoted context omitted.

I’m in the same boat. Plus, the iPad app was not great at the time, which is very important to me (I read and annotate papers a lot on my iPad, it is an ideal device for this). I dug a bit to see if it was likely to be resolved soon, and it did not seem like it. So I find another solution, which in retrospect was a good thing since that was 5 years ago and the situation has not changed since. FWIW I ended up using Bo…

Is this ( https://github.com/iandol/bookends-tools ) the Bookends you referring to ? I don't care about citations. All I need is a PDF organizer have categories / tags and can add notes / make annotations.

https://www.sonnysoftware.com/

Great Papers alternative if one wants Mac/iOS support and relatively good (but not perfect) importing from a Papers library.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#96

Post by hazza_n_dazza »

bonoboTP wrote: post #87
medimikka wrote: post #76

Earlier quoted context omitted.

Mendeley changes certain fields on import to always download its abstract PDF as the reference paper with a link to its paywall. In essence, those things are PDF archivers and citation managers rolled into one. If I were to send you my latest research and you'd import it into Zotero, you'd get a managed citation and my paper. In Mendeley you'd get a managed citation and a downloaded abstract version with CrossRef to…

But Joe Rogan listeners aren't using Mendeley. These issues are separate, but you're angry at both and are somehow mixing them. The paywall can be circumvented via sci-hub. And more and more papers are now on biorxiv and similar. 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…

this isn't about joe rogan, its about someone stealing public medical data

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#97

Post by Ostrogodsky »

I love and I use exclusively Linux but sometimes I despair:

> How do I install Zotero?

Mac Open the .dmg you downloaded and drag Zotero to the Applications folder. You can then run Zotero from Spotlight, Launchpad, or the Applications folder and add it to your Dock like any other program.

After installing Zotero, you can eject and delete the .dmg file.

Windows Run the setup program you downloaded.

Linux Download the tarball, extract the contents and run zotero from that directory to start Zotero.

For Ubuntu, the tarball includes a .desktop file that can be used to add Zotero to the launcher. Move the extracted directory to a location of your choice (e.g., /opt/zotero), run the set_launcher_icon script from a terminal to update the .desktop file for that location, and symlink zotero.desktop into ~/.local/share/applications/ (e.g., ln -s /opt/zotero/zotero.desktop ~/.local/share/applications/zotero.desktop). Zotero should then appear either in your launcher or in the applications list when click the grid icon (“Show Applications”), from which you can drag it to the launcher.

Ehhh, I am not doing all of that.

Wait, there is hope, it also says:

> Debian/Ubuntu-based Distros > A longtime community member maintains zotero-deb, a lightweight wrapper for > the official tarball.

Let's go there!

"PSA

I'm in the process of transferring the hosting of these packages to the Zoero organisation. Until that is done, the following options are available:

download from this repo (re)install using curl -sL https://github.com/retorquere/zotero-deb/releases/download/a... | sudo bash caveat: github has made recent changes to how they're hosting release files, which triggered a long-standing bug in apt. If you hit this problem, see this thread for a workaround. download from sourceforge (re) install using curl -sL https://downloads.sourceforge.net/project/zotero-deb/install... | sudo bash caveat: sourceforge uses a mirror system that updates haphazardly and which may redirect you to a mirror that is down. If you get errors, try again in a few hours."

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#98

Post by BostonEnginerd »

jlduan wrote: post #88

It seems Zotero still doesn't support 3rd party cloud service (Dropbox, Google Drive, iCloud etc). I really recommend Paperpile, especially its Chrome extension. In my opionion, nothing beats Google Docs on collaborative writing.

I believe that they support WebDav.

https://www.zotero.org/support/kb/webdav_services

You also have an option to use the Zotfile extension to sync with other services.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#99

Post by markdjacobsen »

medimikka wrote: post #35

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/ ), which adds better Citekey management and, my perso…

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_beDLtsTm....

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#100

Post by BostonEnginerd »

westcort wrote: post #84
cycomanic wrote: post #80

Earlier quoted context omitted.

You're getting down voted because you comment seems uninformed. AFAIK Zotero is available on every OS that Firefox runs on, for example. Also you talk professional publishing, what does that exactly mean? Zotero is a reference manager, so largely aimed at academic writing (because they tend to be the ones who cité and use references the most). I would be surprised if any other setting has more stakeholders, scientifi…

Let’s say you are working on a paper with 6 coauthors for a major medical journal, hypothetically. Dr. So and so in Russia, another in Japan, a third in California, and a few others. Would you mind reviewing this draft? Oh, yeah, by the way, you need to install Zotero before you can edit the references. How do you think that is going to go? How about dealing with a graphic designer in Hungary who can’t copy the text…

I'm not really seeing it. In most of the workflows I've used, one person is responsible for maintaining most of the document including the bibliography. The other coauthors will add in notes requesting to add in a new item, etc.

Zotero is used primarily for managing the PDF library, the actual writing will happen in Word, LateX, etc. The reference list produced by Zotero is just text.

I don't see any real requirement that everyone working on a project would need to actually use Zotero, though I guess it would be handy to keep a coordinated shared library of papers.

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