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Bibliography Software Mac Review

This is a repost from January 14, 2011. I had thought about doing a new post, but it is still relevant and came up in my conversation with our new Tombros Librarian Chuck Jones and CLA associate dean Christopher Long.

I still find Sente to be most useful for me and their new Sync2 has made it even better and easier to set up the same bibliography on multiple machines (i.e., to share with others). There are new pricing structures with Sente 6 as well. There is a free account with up to 250MB of storage and the iPad app is now free. The Sente app for Mac at full price should only be $49.95, for an academic the cost is even less, $29.95. That comes with 1GB of storage (so far enough for me). You can now also purchase more server space anywhere from 5GB at $20/yr to 100GB for $130.

A few other links have been updated in the body of the post as well.

Original Post:

14 January 2011

I am getting (finally) deeper into my research project on Targum Ruth and needing to organize my bibliography and research PDFs. Now while you all know that I am no luddite I will tell you that database software and bibliographic software in particular is my kryptonite. My brain simply locks up when I try and understand how they work and what is going on. Fortunately I have a very patient and hard-working grad assistant who has helped me through this process.

My PSU colleague Chris Long has written about his “Evolving Digital Research Ecosystem” [Updated post: “Sente, Mendeley, Zotero: Too Many Sharp Tools“] and has long encourage me to consider Zotero and Mendeley. However, see above. Mendeley in particular strikes me as overwrought. Both, however have the benefit of being free. Clearly what I needed to do was to prioritize my needs and consider the options. Like Chris I wanted to close the circle on my digital research process (see my earlier post regarding using the iPad for research) and I think I have found the solution, albeit not a free one.

Criteria for a solution:

  • Available on both Mac and iPad
  • Store both bibliographic information and associated files (images, PDFs, etc.)
  • Allow annotation of PDFs
  • Synchronize between Mac and iPad
  • Integrate with Nisus Writer Pro, my word processor of choice

There are, to the best of my knowledge, only two solutions that meet the first criteria, Papers and Sente. Both have an iPad app (Papers has an iPhone app as well) and a desktop app. Papers is a bit cheaper on the iOS, $14.99 as opposed to $19.99, but Sente offers a free Sente Viewer (does not allow markup). Papers desktop app is $42 while Sente is hefty $89.95. Both offer student discounts but Sente allows you to use the license on up to 3 machines (e.g., my office and home machine and my grad assistant’s machine). So as I said, not free. Fortunately both offer the chance to demo the desktop software for free (something that will not be possible with the new Mac App Store, they will have to do “lite” versions, as in the iOS App Store).

I did not get very far in testing Papers because early on I was told that it only supports journals, not books and does not allow you to annotate PDFs. The first sounds dubious to me (how could they possible not include all forms of bibliographic data?) but the second was a deal breaker. As much as I like iAnnotate I want the benefit of a complete ecosystem. That left me with Sente and so far I can say that I am very pleased.

The best way to offer this review is simply to describe how events transpired. Eric (my GA) took the Bookends1 database that a previous GA had prepared with about 170 entries and we had a folder (shared on Dropbox) of about 90 PDFs. Eric exported the Bookends file into an Endnote format and the imported it into Sente desktop app. Perfect! Everything came right in with no troubles. He then associated the PDFs with the relevant citation/entry. (You can have Sente store these all in a bundle or as a folder that it will automatically organize for you. I chose to have it import the PDFs and organize them for me and I will later delete the original folder of PDFs.)

At this point we were sharing one database file via Dropbox. This works but you need to be careful not to have it open in two places at one. Fortunately Sente has a solution for this: Sente 6 Synchronized Libraries!

Work on your library on any of your computers and always have up-to-date information everywhere. Or, share one library with any number of colleagues, and give each person the appropriate level of access to your data.

I won’t bore you with the details of the process, but suffice to say that I have the main DB on my office Mac (all are actually backed up via Dropbox) and open the synchronized library on my machine at home, as does Eric. I take notes on a PDF, either in Sente app on the desktop or on the iPad and all copies of the PDF update. One major caveat: you must markup the PDF only in a Sente app. You can open them in other apps but the changes will not be synchronized. As Eric adds new bibliography and PDFs all copies of the database update and the various “smart folders” like “recent changes” make it easy to see what my collaborator has been working on. You can also create status tags (and sort by them) so he can flag something as “follow up” and I will see it immediately.

Once you have set up the Sente iPad app you have access to all of your bibliographic material, attachments and all, automatically synced. (You use the iTunes interface to initially add the synced library file and from then on the updates occur over the air, no hardware syncing required.) Inside the iPad app you can highlight, quote, and annotate your PDFs. They obviously have to be OCRd before you add them to Sente to be able to use the quote feature, but even if they are not OCRd or simply are graphics you can use a box tool to lasso the relevant portion (which is then saved as an image in the note) and you can add your annotation as you see fit. You can then send the notes, bibliographic data, and quoted text to someone via an email. I have included a number of screenshots below from the iPad app. I should add that the app can be slow to respond when reading and annotating a PDF. Since iAnnotatePDF regularly warns its users about sluggishness due to large PDFs I am assuming it is a memory issue. It is certainly usable, but does merit some patience at times.

Both the desktop and iPad app make it very simple to add both references and PDFs from within the app using their integrated browser and database searches.

I have not yet tried to use Sente within a paper for citation and bibliography creation. All accounts on the user groups are that it works fine with NWP and is built right in to Mellel. It also integrates well (so I read) with Word.

Everyone has their own work habits and patterns so Sente may not be for you and some will always only insist on using free options. So far I have found it to not only be incredibly solid but a great tool for collaboration. While I am reading an article I can highlight a footnote and send it in an email to my GA asking him to follow up on the references. All from within Sente. (And because Eric is so good, the next day I had a half a dozen new entries in my library with their PDFs!) This is some pretty tight integration and has certainly helped me in my research. YMMV.

 

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February 28, 2015

Thoughts on Reference Management Software

Reference management software is an incredibly useful tool researcher and academic. It solves two problems that are otherwise very frustrating: (1) organizing and searching PDFs of journal articles, and (2) properly formatting a bibliography when writing a paper with citations.

Last week, I tried out several reference managers. (I had been using a combination of Zotero and Bookends, but both had some annoyances.) Here are my thoughts on each, and what I think you should consider if you want to start using a reference manager or are thinking about switching.

Update: July 10, 2015

I’ve found two new reference management options since this post was originally published.

The first is Paperpile. This is Chrome extension that integrates reference management with Google Docs. I haven’t had a chance to try it in-depth, but if it works as advertised, it may be the holy grail of collaborative reference management.

The second is Cite This For Me. This is a tool for generating references section entries automatically from an article title or a DOI. If you end up having to make a references section manually, this is a very easy way to do it.

Update: September 10, 2015

I have used Paperpile now, and it works pretty well. They have a beta Google Docs plugin that I use (rather than their Chrome extension; the Google Docs plugin is compatible with Safari, and I don’t like the security implications of browser extensions).

I’ve completely given up on organizing and searching my references in the same software I use to do citations. I now use DEVONthink for organizing and searching. DEVONthink has very advanced search capabilities, which solves my biggest reference management problem: finding papers that I remember reading, but do not remember the title or authors.

So I can’t speak to the reference organization and searching features of Paperpile, but inserting citations and building a list of references in a Google Docs file works just fine.

Paperpile’s killer feature is that it is built around Google Docs, which makes collaborative writing so much easier: everyone has the most current version of the document, and there is no manual merging of changes from multiple authors. The “suggesting mode” feature in Google Docs is now fairly comparable to track changes in Word, the bread and butter of collaborative academic writing.

Regardless of how you like to organize your references, I definitely think Parepile is worth a look just so you can use Google Docs. (Here’s how I use Google Docs with collaborators to avoid any hiccups with people who don’t regularly use Google accounts.)

Update: September 14, 2015

I just heard about Flow, from the Refworks people (thanks Peyton!). Like Paperpile, it is web-based and integrates with Google Docs. I have not tried it yet myself, so if you use it let me know what you think.

Update: May 22, 2016

ReadCube is another reference manager worth looking at. They have web, mobile, and desktop apps, and also recently acquired Papers, which I cover in detail below. The consumer offerings from ReadCube are funded from their publisher services, so this is not a venture-funded consumer app company without a viable business model that is likely to disappear.

Update: December 7, 2017

An anonymous reader pointed me to colwiz, a reference manager that was apparently started at Oxford. I haven’t tried it, but the marketing page makes it look like a viable alternative to something like Zotero.

Update: January 2, 2018

It looks like Sente (discussed below) may have been abandoned. The developer’s website appears to be down and their Twitter account has been inactive since 2016.

Update: January 13, 2018

Here’s what my current workflow looks like.


Zotero

I’ve been using Zotero to organize and search my references for more than a year, so this is the application I have the most to say about.

Pros:

  • Free, cross-platform. Additional cloud storage is very cheap, and you probably won’t need it.
  • Open source, maintained by a group at George Mason in a sustainable manner.
  • Really good cloud sync (important for backups even if you don’t use Zotero on multiple computers).
  • Good multi-user sharing features, including sharing of PDFs.
  • Integration with Microsoft Word seems to work well (I haven’t used it a ton though).
  • The PaperShip iOS and Mac app.
  • The browser plugin will import citations and their accompanying PDFs from PubMed and many journal websites.
  • Really fast full search of all PDFs in your library.
  • You can add plugins like

Cons:

  • No good way I’ve found to track which articles need to be read, or mark articles for follow-up.
  • Somewhat confusing reference organization capabilities (definitely read the documentation page on this before you try Zotero).
  • Annotations in PDFs are kept separately from notes on a reference written in Zotero: you have to open the PDF to see them.
  • Desktop application is based off of Firefox, so it’s more clunky than it would be as a fully native application. (Long-term, I think this reliance on XULRunner is a big liability. Users will increasingly expect native-feeling applications, which I doubt will be possible without a complete rewrite.)
  • Web interface is mediocre.
  • No internal PubMed search, . Update: references can be quickly added by entering an ISBN, PMID, or DOI. This feature works great.
  • Initial setup process can be very confusing for new users.
  • No built-in PDF viewer/annotation. This works fine for me because I prefer to use the great PDF support built into OS X, but would definitely be a downside on Windows or for Mac users unfamiliar with Preview.app’s annotation support.

Bottom line: I think Zotero would be great if your reference management needs are lightweight, or you’re willing to put up with a few annoyances to use open source software. If you use notes and annotations heavily, or want read/unread/flagged status for references, look elsewhere.

Mendeley

Mendeley is probably the most widely-used modern reference manager. “Modern” in this context basically means that they have modern interfaces, take the web seriously, and have social features.

Pros:

  • Best web interface of any reference manager out there.
  • Cross-platform.
  • Free account tier (limited storage).
  • Widely used, especially among younger scientists.
  • Sync seems to work well in my limited testing.
  • Desktop interface is generally good.
  • PDF notes displayed alongside notes taken in Mendeley, but viewing annotations still requires opening the PDF.
  • Built-in PDF viewer has good annotation functions.
  • First-time setup is easy.
  • The PaperShip iOS and Mac app also works with Mendeley.
  • Social features may be useful.

Cons:

  • Owned by Elsevier, which has a terrible reputation for supporting open reserach. This is a dealbreaker for me.
  • No easy way to import PDFs (i.e. no feature like Zotero’s browser plugin that will automatically import PDFs along with the citation). This is also a dealbreaker for me, because importing PDFs quickly saves a huge amount of time.
  • Additional storage is relatively expensive ($5/month for just 5gb of space; for comparison, Apple provides 20gb for $1/month).
  • Mac app feels non-native in the same way Zotero does. It does not follow standard Mac application best practices. For example, the font size in the main view is smaller than the system font and can’t be adjusted.
  • Social features may not be what you want in your reference managers.

Bottom line: If you can look past Elsevier’s reputation and find a PDF import workflow that works for you, this is a good option.

EndNote

EndNote is probably the most widely used mature reference manager. By “mature,” I mean that it’s been around forever. I used to use EndNote back in college, but it’s changed substantially since then.

Pros:

  • Cross platform.
  • Widely used, so there are citation formats for essentially every journal.
  • Automatic PDF downloading. This feature is amazing when it works. You can select one or more references in EndNote, click a button, and it will automatically download the PDF into your library if you have access.

Cons:

  • Mac application interface is atrocious in recent versions. Watch the first 30 seconds of this video.
  • Costs $220 with education pricing (!!!).
  • Web sync is very difficult to set up.
  • Web interface is also atrocious.
  • Software updates only go one version at a time, so I had to run six upgrades to get from version 7.0 to 7.2. I’m sure there’s a work-around, but this is inexcusable default behavior in modern software.

Bottom line: Zotero and Mendeley both have much better interfaces for much less money. I would try one of these first before trying EndNote. The only stand-out feature in EndNote is automatic PDF downloads, but Zotero’s browser plugin is as good as this in my experience.

Papers

Papers used to be Mac-only, but recently released new comparable versions for both Mac and Windows. They also have an iOS app and a beta web interface. I used to use Papers prior to the latest major release and liked it, but had a ton of trouble upgrading to the new version so I switched to Zotero.

Unfortunately, I still hit numerous stability and performance issues even just using Papers for a few hours. Considering this is their flagship app on their original platform, I can’t recommend any of their apps.

Pros:

  • Hands down best desktop interface for both Windows and Mac.
  • The Mac app is native and follows good Mac application design practices.
  • Good built-in PubMed search interface, which can easily import PDFs.

Cons:

  • Still lots of bugs, performance issues, and crashes with v3 of the Mac app.

RefWorks

This is a web application site-licensed by my institution.

Pros:

Cons:

  • Web-only, and the website feels dated by a decade or more.

Bottom line: Any application in this post is a better choice.

Mac-only applications

Bookends and (appears to be abandoned – see update above) are also options if you use a Mac.

Bookends has a ton of customization options, I found that I needed to do a fair amount of customization to use the bibliography builder, and that the process for doing this was not very intuitive. (I used it because my word processor integrates tightly with it.) It also is clunky in a number of other ways, including a lack of cloud sync. I don’t think there are any big advantages to using it over Zotero or Mendeley.

I really like Sente. It has my favorite sync system of any of the applications I tried and it is the only application I found that combines notes and PDF annotations in the main view. The UI is not as modern as Papers, but comparable in terms of usability. It has a steep learning curve for tagging and was difficult to set up with my library’s proxy server, but it has great documentation. If you can live without sync with Windows users, (appears to be abandoned – see update above).

Final thoughts

I think Zotero is the best general purpose choice. But if you can live with Mac and iOS only, (appears to be abandoned – see update above).

If you can ignore Elsevier’s bad reputation and don’t mind slower PDF import, Mendeley is also a good option.

Note that Mendeley has an option to stay in continuous sync with Zotero. You can use this feature to try out both applications without having to import references twice.

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