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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

#201

Post by tonyg »

kelsolaar wrote: post #193
carbocation wrote: post #48

Earlier quoted context omitted.

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…

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/mendele...

Greydon's page is based on my original article: https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db.

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

#202

Post by Labo333 »

faustlast wrote: post #169
Labo333 wrote: post #161

I tried Zotero and equivalent softwares (mendeley) a few times but never caught. My typical workflow involves a big gdoc that I can share with my advisor. I paste the title, year, author and number of citations (to know which articles are the most influential). And, most importantly, a link to the pdf (sometimes through sci-hub). Then I write notes under those articles, pasting screenshots of equations that I want to…

Workflow: 1. copy doi and extract in into zotero (automatic looks for pdf). 2. better-bibtex (zotero add-on) will automatically generate the .bib entry. 3. tex editor automatically recognize bibtex entry. 4. write all the relevant stuff with proper formatting (ready for paper). 5. git and github for sharing.

that looks very cool!

I found https://gagarine.medium.com/use-sci-hub-with-zotero-as-a-fal... to get the pdf from sci-hub\

Thanks!

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

#203

Post by kuhewa »

CRConrad wrote: post #200
kuhewa wrote: post #123

Earlier quoted context omitted.

Honestly, I am starting to think the open source movement has done as much harm as the subscription model to the scientific information ecosystem. The incentives are so high now to get volume published in pay to publish journals, leading to rushed peer reviews. Also APCs skew who can publish 'well'. The APCs for some top Cell and SpringerNature journals are about ten thousand fucking dollars. Great that the public ca…

> Honestly, I am starting to think the open source movement has done as much harm as the subscription model to the scientific information ecosystem. The incentives are so high now to get volume published in pay to publish journals, leading to rushed peer reviews. 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 th…

oof -- that should have read 'open access' and was intended to pertain specifically to the scientific publishing ecosystem. my bad.

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

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

#204

Post by CRConrad »

kuhewa wrote: post #203
CRConrad wrote: post #200

Earlier quoted context omitted.

> Honestly, I am starting to think the open source movement has done as much harm as the subscription model to the scientific information ecosystem. The incentives are so high now to get volume published in pay to publish journals, leading to rushed peer reviews. 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 th…

oof -- that should have read 'open access' and was intended to pertain specifically to the scientific publishing ecosystem. my bad. 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…

So now the scientists get to PAY to be published?!?

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?)

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

#205

Post by kuhewa »

CRConrad wrote: post #204
kuhewa wrote: post #203

Earlier quoted context omitted.

oof -- that should have read 'open access' and was intended to pertain specifically to the scientific publishing ecosystem. my bad. 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…

So now the scientists get to PAY to be published?!? 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?)

Yeah increasingly scientists have to pay. It has become the 'principled' thing to make the publishers richer in the name of open access. Sometimes there are waivers for researchers from developing countries. Unfortunately funding bodies haven't universally caught up to the expanded $ needs. Nor have institutions.

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.

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

#206

Post by CRConrad »

kuhewa wrote: post #205
CRConrad wrote: post #204

Earlier quoted context omitted.

So now the scientists get to PAY to be published?!? 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?)

Yeah increasingly scientists have to pay. It has become the 'principled' thing to make the publishers richer in the name of open access. Sometimes there are waivers for researchers from developing countries. Unfortunately funding bodies haven't universally caught up to the expanded $ needs. Nor have institutions. There is a model with journals like PeerJ with relatively cheap APCs and a deal where you could sign up f…

> 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? :-)

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