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CUNY Technology Group

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Software for managing research

  • I have been struggling with managing my growing research material, notes on that material, and any writing. And what’s the point of doing work if you can’t revolutionize the process endlessly. Right?

    My research material is scattered between folders of PDFs (on Dropbox) as well as through (which I use as my primary bibliography manager and also store on Dropbox).

    My notes are either in Scrivener project files for papers I’ve written in the past, in Evernote, or as plaintext files (markdown). And my shorter journal writing is either in Scrivener projects or plaintext (markdown) files. I’d like to consolidate this a bit to make managing it… well more manageable. I wondered if anyone had similar struggles and advice.

    I see three solutions:

    1) PDFs and text files organized in folders without depending on any specific software for managing either
    2) A single Scrivener project as a research journal where all my notes and writing would be stored. Continue to manage PDFs through
    3) A private file-based wiki/blog (e.g., Gollum)

    I am leaning towards the 3rd option.

    How have others used (desktop or web) software for managing their research?


Viewing 9 replies - 1 through 9 (of 9 total)
  • I use Google Drive and Google Docs for everything. They recently reduced the price for a 100GB plan to $1.99/month. They also just enabled Add-ons to docs (, which includes a 3rd party software called EasyBib. The simple version can look up citations in the document window, and if you want more advanced options, there is a $20/yr upgrade. I just started using it, and there are some sources I have to manually cite, but overall it seems to do the trick.

    My personal organization system is to save everything to folders named with year first, then class abbreviation or project name. I create a folder called “_old” within each folder. The underscore means it will sort to the top, and I occasionally move obsolete stuff to the old folder that I don’t want to delete, but want out of sight. Then I archive years as they pass…

    I use a very low-tech system that combines (1) and (3). I mostly rely on the filesystem to organize materials, and I use a wiki for notes.

    The wiki I use is potwiki, a Vim plugin. That means the wiki lives in my writing environment, so I don’t have to jump into a browser to use it (the idea being that I cut out a potential source of distraction). It also means that the wiki is text only; I don’t really require functionality to embed images, etc. I use a combination of markdown (for notes) and bibtex (for bibliographic data).

    In Vim, I also use a project tree so I can quickly access important files (such as interview transcripts) in my filesystem.

    (A screenshot of what that setup looks like.)

    A while back I created a file naming convention for my office to help us keep all files organized. Hope you find it useful.

    For cloud storage you can use, as others have pointed out, dropbox, Google drive, SkyDrive, etc. (I personally use the first two)

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    I use Zotero for my references. The ZotFile plugin allows you to manage the PDF naming and folder structure. I’ve blogged about this here:

    You can do notes in Zotero, but IMO the notes are kind of “buried” in the entry, so I don’t use that feature very often. I keep writing notes, meeting notes, process documentation, project planning, etc in a mind map, specifically Freeplane ( I also write (dissertation, articles, lab exercises) in Freeplane because it is easy to create nodes for notes and ideas while other nodes are more polished content, but all visible in the same document.

    The is a project named Docear ( that tries to integrate research notes, PDF library management, and composition by combining Freeplane with Bibtex and adding a file management capability. It is a pretty young project and I like the idea, but I didn’t find it that useful in practice. YMMV.

    The CUNY libraries all subscribe to RefWorks, which is more helpful for bibliographic metadata management than it is for document management. You can save pdfs in RefWorks, but it is not very elegant. However, the RefWorks vendor, Proquest, is now offering a new product called FLOW ( which has a very easy interface and is good for storing and sharing documents. FLOW is offering individual researchers free accounts. They are also offering institutional accounts that have more features, including, on the user end, the ability to share with more than ten others.

    At Brooklyn College we are deciding whether or not to subscribe to FLOW. We have a lot of users committed to RefWorks and they could migrate their citations and pdfs without much trouble if we get the institutional version of FLOW. As with any proprietary source, though, there is a fee, but there is also stability.

    We are having the vendor come and demo FLOW at the Brooklyn College Library on April 22 at 10:30 am. All are welcome to attend.

    At BC we have also seen a lot of users switching over to Mendeley (, which is free, but now that it is owned by the very large publisher Elsevier, it may not stay free.

    The librarians on your campuses are up on all of these tools. I’m sure anyone of them would be happy to recommend something that has been successful for others.

    This site does some useful comparisons:

    Hope this helps.


    Thank you all for the comments!

    I have been resisting giving up Papers for my reference and pdf management. But they have moved onto a new version, which means I’ve gotta either upgrade or give up. I actually played with BibDesk, a mac front-end for bibtex libraries, and thought it worked really well. Zotero also seems worth trying, especially because it support some collaboration.

    But it seems a lot more has been done on the reference and pdf management end, whereas organizing research notes is still something each of us end up having ad-hoc solutions for. That makes sense given how particular research workflows can be. Like John Boy, I am most happy dealing with text files in an editor like Vim. So a file-based solution for research notes would be preferable. Most of my writing the past few years has been in markdown which I convert to other formats using pandoc, a great tool written by a philosophy professor. The nice thing with pandoc is that I can give it a bibtex file, which allows me to use citation keys as short hand for references in my document and then pandoc generates a bibliography from the keys I used in any given document. I have even set up my Scrivener in such a way so that I get to still use pandoc (though I find Scrivener overkill at times). It can be a bit of a headache but I much prefer it to loading up Word or Google Docs. What I am missing though is how to organize my many text files. Folders might be enough, but most of the time I want to grab a file without regard to how I might have previously organized it. Or maybe one file makes sense for multiple topics. Categories and tagging seem more appropriate for research entries.

    John Boy, I was looking actually at vimwiki. The problem is that it has its own wiki markup syntax, whereas I’d prefer to use (pandoc) markdown.

    Beth, just signed up for Flow. My immediate sense is that it’s fairly polished and a lot better designed than Zotero. The rates for extra storage on Zotero seem comparable to what one gets from Flow. I guess the big difference is that Zotero is an open source project whereas Proquest’s Flow is clearly not.

    Another great thing about Google Drive is that if you use in conjunction with Chrome, you can sign into the browser, so it remembers your history (bookmarks, passwords, etc.) wherever you’re signed in. So, for example, once I’m logged into Chrome, if I want to pull up a document I work on frequently in Google Docs, I can just type the file name into the url bar, and it will come up as one of the suggested links. It is possible to install Chrome on all the GC computers (PC’s only) for your user profile without an admin password. You can upload entire folders to Drive if you have Chrome installed, which is not possible w/ Firefox or IE.

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