As a researcher I always appreciate to see new opportunities to organize my work and improve my routines. This system does seem interesting.
To this day though I've found that Zotero is unbeaten to keep everything organized. I collect all my notes and documents in the Zotero library, and I sync it on multiple devices by placing the Zotero files in a Dropbox folder.
In this way I can use whatever app I want to write the actual notes (MD, txt, docx, whatever). I organize the notes in Zotero "folders" and the documents of each note are stored in "sub-folders". The best thing is that these are not actual folders, so the same document, if relevant for multiple researches, can be placed in two or more folders/sub-folders etc.
This setup has worked for me for nearly 8 years, with over 50 publications and over 5000 documents in my Zotero library. And best of all, the only thing I'm actually paying for is Dropbox, which I would anyway and, IMHO, is totally worth it. But that's another story. And more importantly, to get things started one can rely on the free tier of Dropbox, so even that's free.
So as a researcher (which translates to little money to spare and high volumes of documents to manage), I find that to this date I still have to find a solution that beats my configuration. I would love though to discover new opportunities!
Your comment resonated strongly with me, for I am also a researcher who finds zotero and dropbox to be a very helpful combination. (I use dropbox to store PDFs of documents, rather than using zotero, because I already pay for dropbox and basically want to avoid the paperwork of yet another bill.)
However, I do not use zotero notes much at all (apart from taking notes on bibliographic elements), and so I am hoping you might write some more about the mechanics of how you do that.
I am particularly interested in how you handle cross-references. I tend to use markdown and wiki approaches, because they make it easy to have inline cross-references to other documents. Is there a way to do that with zotero notes, other than using the "Related:" and "Tags:" items at the bottom of a note?
Also, do you have hints on organizing folders of notes?
Since you've been doing this for years, I can bet that you have some great advice, and I hope you can spare the time to explain your procedures in a bit more detail.
As a researcher too, I understand exactly what you are saying. I prefer DevonThink[1] to Zotero for searching and organizing over tens of GB of data with tens of millions of words. Works with the native Mac filesystem, so you don't have to import into the app if you don't want to. Automatically archiving my entire email history is a huge plus. Finds everything in milliseconds. Mac only.
It's very versatile — it's got great image handling, for example, so you can use it for collecting visual materials, and easily browse as a gallery or as full-sized images. And I particularly love the built-in PDF support, which has everything you need — multiple reader views, annotations, table of contents, rotation, conversion, OCR, etc. Search is fast, multiple database support is great. And it's a very nice touch that you can combine the local database file support with cloud sync, although the mobile app could be better there.
It's worth noting that Devonthink does not have citation/reference management, so for scientists/adademics it's probably not an adequate replacement as Zotero, Endnote, Papers, etc.
Annotations become part of the PDF file on disk. But they're stored as separate editable objects in the PDF that remain editable; for example, if you open an annotated PDF in Preview (on macOS) or in Adobe Reader, they are still editable. And so you can remove them.
Devonthink also lets you remove all the annotations. With your PDF(s), select Data > Convert > "to PDF without Annotations", and it will make a copy that has all the annotations removed.
I agree that it would be nice to keep the annotations separate. But fortunately the PDF format is flexible enough that it can preserve the annotations and not "hard code" them into the visual tree.
You can’t even export pdfs or notes from it anymore to send to others. Only some snippets via some bad Elsevier platform which is a headache. They will lock you in, and they specifically updated Mendeley such that the database is encrypted towards you yourself. I lost my whole Years worth of papers and research to it.
Do not use Mendeley.
Do not use anything made by Elsevier.
If you run a lot of cross platform software, the Mac may be the perfect machine for you. It can (legally) run more software than anything else - MacOS, Windows, Linux - though a combination of dual booting & virtualization.
Great points! I also use Zotero extensively. I used to store files on Box previously because of WebDAV but they dropped that support a year or two years ago.
Now I pay for unlimited storage on Zotero. This is for two reasons: 1) They recommended supporting them by buying storage rather than donating directly. Maybe it has changed now but I continue with my subscription, 2) I have several co-authors with whom I share my documents. Most of them don’t have a paid Zotero subscription. But shared folders don’t eat up their personal storage limit unlike Dropbox.
Zotero is a lifesaver for organising articles and documents. I also pay for storage as a way to support the project. Their new web-client is quite nice.
Dropbox (or any of the other syncing apps) as a syncing mechanism for other stuff is underrated IMO. I personally have notes, password manager database and a budget app database synced between devices and the amount of value I've derived from having everything automatically sync between devices is huge.
I wish more apps would take the wide availability of "magic syncing folders" into account when designing their data storage. (I know many VC funded apps would prefer to keep the data in house so it can be monetized, but there is less excuse for open source tools)
I don't like to involve cloud apps in my workflow because there is no guarantee when what will change and then break my workflow. I currently self host a simple note server[1]. Now cloud apps can help me sync these notes across my devices but I would rather prefer mapped drive than cloud sync.
I take notes from my mobile/desktop browser address bar or simply edit the files directly. No dependencies, no cloud storage, only files and no one can ever access them but me. Works like a charm for me.
I agree but there's no great cross-platform syncing solution yet, to my knowledge. Dropbox dropped all linux support except ext4, which is limiting. GDrive and OneDrive don't have a Linux Client. Nextcloud is neat, but still not very well supported (eg, by android apps).
The result is I'm using a mishmash of all those, and keep forgetting what is synced where.
For Google Drive there is a solution for Linux [0].
I actually really like it, it's not automatic, but that's not really a problem, because you can make it automatic with some bash and crontab.
Is it because you’re assuming a cloud backup is necessary component of syncing solution? In that case, you can just designate one of your synced devices to keep backups to S3/B2 :D
I've been using pcloud on Linux, and I've found it to be fast and easy. Comes with a lot more free storage than Dropbox. I believe you do have to be willing to install their client.
I think dropbox (or any “magic folder” sync) is great as well.
YouNeedABudget used to do this and then “upgraded” to use their own proprietary service that charges $X/month.
I think it’s not just the data monetization, but that frequently data sync is the only feature that requires ongoing services. So if I write software and want to charge a monthly service fee, then data sync is where I can force the service.
Companies can do whatever they like, but jerk companies will make poor designs that require their own magic sync. Smart companies should fall back to a sync folder to allow self-run and just charge me for software.
“magic folder” sync always meant https://syncthing.net for me. Once set up it syncs in LAN, over slow connections, with lots of changed files, handles concurrent syncs, hundreds of GBs of data etc. – it's great and becoming better day by day.
I never understood how to do this. You just drag and drop a document, and after that only one consistent copy is maintained?
Also how do you have documents with inline images? Is it possible to cite other documents from zotero -- let us say you are creating a literature review?
Not sure what you mean by "documents with inline images", but yes, that's how it works. There's also a handy browser plugin to import web pages/pdfs into Zotero, with automatic metadata.
Yes, you can cite documents you have with zotero by having it generate a pre-formatted citation or a bibtex entry.
Thank you. Let me explain what I mean by "documents with inline images". When i take notes, I want to include screenshots of different pages (may be some pictures or pictures of equations) as inline images. AFAIK, zotero does not sync the inline images entered in notes.
To this day though I've found that Zotero is unbeaten to keep everything organized. I collect all my notes and documents in the Zotero library, and I sync it on multiple devices by placing the Zotero files in a Dropbox folder.
In this way I can use whatever app I want to write the actual notes (MD, txt, docx, whatever). I organize the notes in Zotero "folders" and the documents of each note are stored in "sub-folders". The best thing is that these are not actual folders, so the same document, if relevant for multiple researches, can be placed in two or more folders/sub-folders etc.
This setup has worked for me for nearly 8 years, with over 50 publications and over 5000 documents in my Zotero library. And best of all, the only thing I'm actually paying for is Dropbox, which I would anyway and, IMHO, is totally worth it. But that's another story. And more importantly, to get things started one can rely on the free tier of Dropbox, so even that's free.
So as a researcher (which translates to little money to spare and high volumes of documents to manage), I find that to this date I still have to find a solution that beats my configuration. I would love though to discover new opportunities!