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Zotero: Personal Research Assistant

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Re: Zotero: Personal Research Assistant

#141

Post by bloopernova »

Chris2048 wrote: post #30
bigbossman wrote: post #17

The problem with this (and Mendeley, Papers, Bibtex, etc.) is that each paper/thought is isolated. Roam Research ( http://roamresearch.com/ ) is my new jam.

How does Roam differ from a wiki app like Zim/Tomboy?

Roam is way of using a wiki. i.e. you could quite easily set up a wiki to act in much the same way as Roam.

The journal part of Roam, the page-per-day part, is very useful. You write down what you're doing each day, use tags and links to build up a second brain, so to speak.

Let's say, today I'm working on kubernetes. I add a tag for k8s, which is a link to the k8s page, where I have all sorts of interesting links and notes dumped. When I'm on the k8s page, I also get a list of pages that link to the k8s page, which helps me to remember some other subject that might be relevant.

It uses the Zettelkasten Method: https://zettelkasten.de/posts/overview/ and you can also get a lot of value from reading "How to Take Smart Notes" by Sönke Ahrens.

The value also comes from it mirroring your thoughts and experiences, as I said, the second brain thing.

(I'm terrible at explaining stuff, sorry :( I hope I didn't bore you to bits)

Re: Zotero: Personal Research Assistant

#142

Post by bloopernova »

asdff wrote: post #42
bigbossman wrote: post #17

The problem with this (and Mendeley, Papers, Bibtex, etc.) is that each paper/thought is isolated. Roam Research ( http://roamresearch.com/ ) is my new jam.

What exactly is roam? The website tells me nothing. Zotero has folders and tags for organizing your thoughts how you like.

See my comment reply to Chris2048 below your comment.

It's a wiki like system that helps you to create a second brain of sorts. You write down what you do, and link between lots of different pages, such as "aws" to "ec2" to "vm" to "vmware" to "vmotion". Roam (and org-roam, an Emacs module that I use) shows you what links back to a page, which is incredibly helpful for remembering knowledge and how things fit together.

Re: Zotero: Personal Research Assistant

#143

Post by jmiserez »

mncharity wrote: post #127
jmiserez wrote: post #72

Earlier quoted context omitted.

To be fair, that's a pretty nice link, not many companies provide such an overview. And most (all) of those features are useful things that you'd probably actually want to enable in daily use. And Zotero can run completely offline, without an account. Now compare that to Zotero's biggest competitor: https://www.mendeley.com/terms/privacy

Indeed. There does seem an issue of what baseline to use. Elsevier isn't usually thought of as a useful ethical baseline, but here it's a displaced competitor. Companies embed a variety of telemetry. And while much open source doesn't, some does, and this is perhaps increasing. And yet, if say Firefox always maintained an open but empty connection to mozilla, would it be adequate to suggest "well, no, that's not unde…

Well Firefox actually does (Web Push API): https://support.mozilla.org/en-US/kb/push-notifications-fire...

>Firefox maintains an active connection to a push service in order to receive push messages as long as it is open. The connection ends when Firefox is closed.

I see what you're getting at, but I think the harshest criticism should be reserved for the worst services: those that actually hold your data hostage, don't provide an export functionality and use your data in all sorts of unethical ways.

Organisations that actually honestly do value privacy and try to make an effort to get it "right" should be given the benefit of the doubt and constructive criticism, as they might actually listen. In many cases the feature may simply be driven by convenience and the competition (e.g. cloud storage, accounts, sync), and having a toggle for those is the best you can do if they want to stay relevant. In other cases the privacy issue may have simply been overlooked and the feature is improved (IIRC Mozilla has had a few of these).

Maybe a big red "offline-only" toggle would be great, but the absence of that button does not in my eyes disqualify Zotero from being a great offline solution.

Re: Zotero: Personal Research Assistant

#144

Post by chapium »

tobias2014 wrote: post #8

I've used Mendeley Desktop for some time, which I believe is very similar in functionality (but proprietary, yes Elsevier!): https://www.mendeley.com/download-desktop-new/ Furthermore I think http://www.docear.org/ deserves to be mentioned as another free open-source solution with some interesting mind-mapping functionality: http://www.docear.org/software/screenshots/

This is one of those cases where the "evil" side has a superior product. Imagine if Elsavier were a little nicer.

Re: Zotero: Personal Research Assistant

#145

Post by superlopuh »

I've started using Calibre for these purposes, saving papers from arXiv to it, and can definitely recommend. It takes a bit of manual effort to add tags to the papers, but once you have a bit of a collection going they autocomplete. The only downside is lack of read/reading/unread status, but I've hacked around it by rating papers and books I'm currently reading one star. I'd love to have an easier method for importing the papers, but not enough to actually have tried to write the script yet.

Re: Zotero: Personal Research Assistant

#146

Post by cycomanic »

bigbossman wrote: post #17

The problem with this (and Mendeley, Papers, Bibtex, etc.) is that each paper/thought is isolated. Roam Research ( http://roamresearch.com/ ) is my new jam.

The best application that I ever used for this was docear. Unfortunately it's not being developed anymore and some other things make it a bit painful to use. I'm still waiting for someone to integrate mindmaps with reference management in a better way.

Re: Zotero: Personal Research Assistant

#148

Post by elcomet »

autocorr wrote: post #122

Zotero is simply a wonderful tool and I'm very grateful to the developers for it. As an academic, it is the only GUI program besides Firefox that I consider essential on one of my computers. Some of the features I enjoy: * free software * Linux and multi-platform support * browser extension "that just works" for ingesting items and magic lookup tool for DOIs and arXiv IDs (and I hardly ever have problems with the met…

> I then keep a primary repository of notes in a flat folder with links between them and the literature notes as my makeshift Zettelkasten

Could you give more details about this ? Do you sync the notes to a folder ? How do you do this ? And how to you browse your notes ?

Re: Zotero: Personal Research Assistant

#149

Post by mncharity »

jmiserez wrote: post #143
mncharity wrote: post #127

Earlier quoted context omitted.

Indeed. There does seem an issue of what baseline to use. Elsevier isn't usually thought of as a useful ethical baseline, but here it's a displaced competitor. Companies embed a variety of telemetry. And while much open source doesn't, some does, and this is perhaps increasing. And yet, if say Firefox always maintained an open but empty connection to mozilla, would it be adequate to suggest "well, no, that's not unde…

Well Firefox actually does (Web Push API): https://support.mozilla.org/en-US/kb/push-notifications-fire... > Firefox maintains an active connection to a push service in order to receive push messages as long as it is open. The connection ends when Firefox is closed. I see what you're getting at, but I think the harshest criticism should be reserved for the worst services: those that actually hold your data hostage, d…

Wow. And agreed. One question, re "being a great offline solution", in what sense offline? Able to work without net?

Thinking about dstillman's reply, I was thought-crawling towards a "local/remote vs online/offline" distinction. So Zotero would be local but always online (if net is available). Versus my expectation that when using only local resources, a local tool will be offline.

Re: Zotero: Personal Research Assistant

#150

Post by souterrain »

autocorr wrote: post #122

Zotero is simply a wonderful tool and I'm very grateful to the developers for it. As an academic, it is the only GUI program besides Firefox that I consider essential on one of my computers. Some of the features I enjoy: * free software * Linux and multi-platform support * browser extension "that just works" for ingesting items and magic lookup tool for DOIs and arXiv IDs (and I hardly ever have problems with the met…

I love Zotero for my academic work, but I'm contemplating using it more for less formal research as well.

As Luhmann did, I'm trying to more frequently write summaries of articles—both actual academic articles and things like blog posts, news articles, even recipes. I prefer to handwrite these notes.

For web links, I was thinking of using pinboard's caching feature which assigns a url like https://pinboard.in/cached/01234567890a/ and recording down the 48-bit identifier.

Alas, what happens when my online service of choice fails? So, maybe the Zotero citation key?

I'm wondering what others' experiences are with hybrid written/digital research workflows, and cross-referencing. Anyone have a "personal DOI" that works really well?

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