I have a good memory, but some of the fields I'm working in (NLP, Semantic Web, Information Visualization, Machine Learning) are quickly expanding.

While I do have a good method of keeping track of good research (I only follow the best researchers and research groups on Twitter, Scholar, conferences, journals, etc), sometimes perhaps it's better to save all the interesting papers, add notes to them and put them in context and relationships with other papers (if a paper frequently cites another paper and is a sequel to that paper, perhaps it's better to read those 2 papers together, for example). Essentially the things I want to do are these:

  • keep records of the workshops, classes or tutorials I attended, but also video recordings of presentations I have never seen in real life
  • annotate PDFs, extract metadata from them and generate bibtex bibliographies
  • keep tutorials in pdf + video format synced (where possible)
  • keep everything in context - organized in folders, tagged,
    cross-referenced if possible (if an article is cited in a paper and I already have it in my library, I want to be able to access it fast)
  • I want to be able to search about various keywords/tags regardless of the location where the actual files are stored and OS.

I noticed most of these things are doable in the Apple ecosystem (iTunes, iBooks, etc), but not really on Windows and Linux. Does anyone has any idea about how to do this in Linux and Windows? I happen to absolutely need to use both operating systems (still have some work with SQL Server, Excel, etc), but most of my development work is in Linux (coding in Java, Python, JavaScript and others, but also writing papers in LaTeX).

I would preferably only sync a huge zotero (or similar) folder using Dropbox, and papers/tutorials should be in sub-folders named after their research field, but also tagged so that I can find them regardless of the folder.

EDIT: I have paid Dropbox, but apparently finding free WebDAV is an issue (therefore that would mean an additional 5-10 euros per month). As far as code goes I use GitHub and GitLab.

After seeing your answers, it occured to me that I'm thinking about it too much. Perhaps the best idea is this: the whole workflow should be a webapp - this way it will perform almost similarly on all operating systems, as even if there are differences between browsers, they are not so big as the differences between OSes.

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    You mention Zotero, which does all that, including managing PDFs, subfolders (logical directories, inside Zotero), tags, etc. You don't need to use Dropbox w/ Zotero, a webdav works better and you can get for free one w/ 10GB of space (I'll put the potential spam in the next comment so that it can be flagged and removed if you think it should, without removing this comment). – Trylks Dec 2 '14 at 10:53
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    I think this question is a better fit for the Software Recommendations site. – aeismail Dec 2 '14 at 11:24
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    @aeismail I agree it's a good question for Software Recommendations, but it's also a very common concern for academics as most of us have at least two computers. – Moriarty Dec 2 '14 at 11:28
  • @Trylks - thanks for the invite. I can't use it though as I don't know Russian. If they don't have an English version, I won't use it. I agree with you that Zotero does almost everything I want - except it keeps each file in its own folder which is painful! I want files grouped in folders based on the main subject, not each file in its own folder. Syncing with WebDav sometimes makes your files impossible to navigate outside the plugin you use (for example they can have cryptic names like 0143254afgf1543). – paxRoman Dec 3 '14 at 8:16

Here's what I do, to manage everything between a Mac laptop and a Linux desktop. I usually write code and do heavy lifting on the Linux machine, but when at home or reading / writing documents I use OS X.

  • All files of a manageable size are synchronized with BitTorrent Sync. You could also use Dropbox, but that costs money for >2 GB. BTSync is free, unlimited, cross-platform, and peer-to-peer.
  • If I'm writing code or TeX using TextMate on my Mac, but executing it on Linux, I just run rmate on a document on my Linux machine and the file pops up in TextMate on my Mac. It's wizardry, I tell you. It beats waiting 5-10 seconds for cloud synchronization to catch up.
  • I use Papers3 for my paper library, which synchronizes with my iPad. All the PDFs are kept in my small, free Dropbox account - the file organization is a bit obtuse so Papers3 is in practice Mac/iOS only. Papers3 does have a Windows app, but not Linux. Mendeley will sync with its Linux and Windows apps, so that might be your best multi-platform option for document storage and annotation.
  • I have not used Evernote recently, but it runs using Wine in Linux. That's another option for syncing notes and documents.

I'm not aware of a tool for Linux which comes anywhere close to Spotlight for Mac. If there is a program that will synchronize file tags and such across operating systems, I'd like to know about it! Otherwise, for advanced "metadata" and such you're usually restricted to the ecosystem of a particular application.

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    For code, including LaTeX I use Bitbucket (and I have invitations for that too, but maybe that's going too far...). – Trylks Dec 2 '14 at 11:28
  • @Moriarty I use LaTeX, and Kile does miracles in Linux. I also use GitHub and GitLab. As far as anything Apple goes, I will never buy their products because they costs twice they should cost, and they sync everything (I don't want my pictures from the phone to be accesible on the Mac, for example - except if I choose to do that). I know about Papers and I love it, but there's no Linux version! I have a Dropbox, but even so syncing with Zotero on my own terms is a disaster (I want multiple folders, not each file in its own folder, ...). – paxRoman Dec 3 '14 at 8:19
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    @paxRoman Ah, I mistook your comment about Apple in the original question to mean that you had a Mac but also used Windows/Linux. By the way, you're mistaken - you can choose what things on a Mac you want to sync, and you have to explicitly switch syncing on. But here is not the place for that argument. Just be aware that most companies which provide you with a free service are making money from you somehow. I assume that any personal data I store with a free service is public domain. – Moriarty Dec 3 '14 at 8:51
  • @Moriarty Ok. Good to know. They're still expensive products. Yes, I am aware about this "no free lunch" policy. I would like a browser solution to be honest, and I wouldn't mind if I had to pay for it if it provides all the things I want. Otherwise Zotero + Dropbox synced via good WebDAV (though I haven't found such thing yet) might be the only thing on Linux :( – paxRoman Dec 3 '14 at 8:56

The fact that you use multiple operating systems is really a red herring. All of your competing work flows (Excel, Java programming, etc) can be done both in virtual machines and via remote desktop. Virtualizing a Mac is probably the hardest, but within a Mac you can create a virtual Windows Machine for Excel and a virtual Linux machine for Programming. If you have reliable network access, you can just remote desktop to the different machines.

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    I totally agree with you that the workflow I want it's perfect on Mac, however a my configuration on a Mac costs more than double, and I really don't see why i would throw 3500 euros through the window. I am against anything pricey by choice (Macs, iPhones, iPads). Ideally the workflow should be a webapp. – paxRoman Dec 3 '14 at 8:02

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