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In 2007, a talented pair of scientist-programmers called Mekentosj released Papers, a Mac OS X app that did for scientific literature what iTunes did for music. They followed the desktop version with an iOS app that works as a standalone program or in conjunction with your Mac. The combination of Papers with an iPad is pretty good when it comes to catching up on your reading. Still, that was then and this is now, as they say, and a new and rebuilt Papers 2 is here to take over your research management needs.
Yes, new and rebuilt. Papers 2's innards have been redone from the ground up, and as we'll see in a bit, this has resulted in some teething trouble. Despite the internal changes, Papers 2 still has the same great Mac user experience that has won the company both Ars Technica and (several) Apple Design Awards.
Adding papers works in the same way it did before. If you already have a paper, you can drag and drop your PDFs onto the icon or the app. You can also import them from the search function, which works as a front end to a range of databases and repositories, including PubMed, Google Scholar, arXiv, and more. You can also now import directly from a scanner, which is a neat touch. If you're an existing Papers user, you can transfer your current library, and bidirectional syncing with iOS devices will also let you copy over data from your phone or iPad. For new users, Papers 2 will cost you $79, with a 50 percent discount for existing users, as well as price breaks for undergraduates—site licenses are also an option.
Feb 20, 2014 TL;DR; Go with a cheapest 15” Macbook Pro with 4 cores. I’ve used 13” for iOS development for some time, and switched to 15”. The difference is night and day. It’s incredibly different that it’s super odd that no one really talks about the real di.
Unlike in 2007, Papers is no longer the only game in town in 2011. Probably its closest competitor is the cross-platform Mendeley, which we've looked at in the past—and that's still the best option for those of you who don't use OS X. Mendeley also had some features that Papers didn't; it supported a much wider range of documents than just scientific papers, and has social networking functions that allow you to find and share papers. Thankfully Mekentosj doesn't suffer from not-invented-here syndrome, and Papers 2 has adopted some of these.
In addition to journal or newspaper articles, there is now support for patents, bills, laws, reports, and even media files. Back when I reviewed the first version of Papers, I wouldn't have appreciated how useful this is. Since moving into the field of science policy, however, the expansion of categories has proved invaluable, and gives Papers 2 an appeal to researchers beyond the life sciences.
- Sep 04, 2019 A guide containing recommended apps for research, ebook reading, and document storage, sharing, annotating and citing.
- Jan 07, 2020 Slack is a must-have app for anyone working remotely with others. It is the best business chat app around. The Mac app is a chat window, so you can keep your conversations going without having to log into a web browser every time.
Another feature that seems inspired by Mendeley is Livfe (pronounced 'life'), which brings social networking features to the app. I can't really comment on how it works as it has been closed to the bulk of Papers 2 users since the app launched a couple of months ago.
Probably the coolest new feature is Magic Manuscripts. You can throw away your copy of Endnote, because Papers 2 now integrates with most Mac OS X word processors (particularly Word and Pages) to let you find references, cite them in your document, and format bibliographies. Manuscripts runs in your menubar, and is activated by a keyboard shortcut that brings up a little search window that floats over your Word or Pages document. Papers will also keep track of different manuscripts you have or are working on, which is a neat touch. It integrates well into your workflow and is probably worth the upgrade price on its own. I'm a giant fan.
Unfortunately, it's not all kittens and sunshine. Because of the completely rewritten back end, lots of functionality from Papers 1 hasn't made the jump yet. For one, there's no way as of yet to merge authors or publications. This is really quite annoying, because JM Gitlin is considered a different author from Jonathan M. Gitlin. Likewise, differences in abbreviations of journals result in multiple entries. This function will be added back, but it cannot come too soon.
Another really neat feature of Papers 1 was the ability to see the most recent 50 publications for each journal, which was a great alternative to subscribing to the journal's mailing list. This is also currently missing, although it too should reappear sooner or later. Being able to save custom searches is also currently missing, but bringing this back (as well as better DOI searching) remains high on the list of things being worked on, according to Alex Griekspoor, one of the original pair behind Mekentosj.
![Mac Mac](/uploads/1/2/5/3/125382370/667856240.jpg)
Best Mac App For Research Center
Support for users with multiple computers is still not where I'd like it to be. Mendeley uses a central server to store your database, which means you can keep your home and work computers perfectly synced. My current workaround involves using my iPad to shuttle references from work to home, which works pretty well. In the past, users have put their Papers database in a Dropbox folder, but this is not recommended. As with the features above, multiple computer support is also on the to do list for Mekentosj, and the furious rate of point upgrades—we're already at 2.0.6—tells me that they're not resting on their laurels.
So, should you upgrade? If you'd asked me when the app launched in March, I'd have said not just yet. Now, though, I think that enough functionality has been restored, and the added features are enticing enough, that you should take the plunge.
For the past few months I have been researching some research apps…
On our sister site, The Focus Course, I recently wrote an article detailing my process for how I build my own, alternate index of notes and ideas when reading a book.
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You can get much more detail in the link above, but in a nut, an alternate index is no more than something you list out in the back of the book you’re reading that you create and update as you read through the book. It’s a list you create in real time that is comprised of the book’s themes and topics that most resonate with you, as well as the pages that have the best quotes and ideas around those topics.
![For For](/uploads/1/2/5/3/125382370/658327967.png)
Within that article, I dropped in a brief aside about my desire to begin organizing the notes, highlights, and takeaways from the books I read into a digital database of sorts. As such, I’ve been looking at different research apps to find just the right one.
I’ve been writing for a living since 2011, and despite my greatest fears, I’ve never had a shortage of ideas. For nearly a decade all of my ideas and notes have been kept in Simplenote, but for the past year or so I’ve been wanting a system that is just a little bit more complex than what I’m currently using.
In short, what I’m looking for is something to store all of the ideas, bits of inspiration, notes, quotes, takeaways from the books I read, and more. (Something akin to Ryan Holliday’s notecard system — but digital.)
Since I’m already creating an alternate index of ideas in the back of each book I read, what I’d like to do is create a digital and universally-searchable version of that index: a single repository to organize, sort, and search all my highlights and notes.
As you can imagine, there are a LOT of notes and research apps out there that do this. The issue wasn’t finding an app that was capable — it was finding an app that works for me and my workflows.
I want to do more than simply jot down my ideas and notes. I also want to have them compiled and structured (rather than a giant list sorted only by modification date), but not wholly cut off from one another.
And I also want some pretty fancy search capabilities. For instance, I’d love the ability to bring up all the highlights related to “focus” from all books I’ve read. Or, perhaps, to view my notes and highlights related to “time management,” but only from those books that are about entrepreneurship, and then compare those same notes and highlights against books that are only about creativity.
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That said, here are a few of my initial thoughts on some of the different notes and research apps out there today.
- Simplenote: This is the app I’ve been using for idea capture and other miscellaneous note taking since it shipped nearly a decade ago. I love how easy it is to use, how — ahem — simple it is, and how reliable the sync is. But for my current use-case, I’m looking for something that can handle images and has a more robust folder structure beyond just tags.
- Bear: If you haven’t tried out Bear, you really should (Mac / iOS). It’s spectacular (and may even replace Simplenote for me). You can insert photos into notes in Bear, but otherwise it’s still pretty simple. That’s not a knock against the app — it is simple by design. But that means that, for my needs in this case, it’s too simple to be my go-to research app.
- Day One: This app is one of my all-time favorites, but, as with the aforementioned apps, Day One is not built for what I need in this scenario.
- Apple’s Notes App: There is a lot to love about the Notes app (and even more once iOS 11 ships). You can drop all sorts of cool things into a note, and even draw and sketch, and more. But the search and sort functionality within Notes is not quite what I’m looking for.
- Evernote: I love the power of Evernote and its strong emphasis on making idea capture as easy as possible, but I don’t love the way it ruins the formatting of my text and the way all my content is a silo inside the app. There are many, many smart folks who use Evernote, but so far, for me, it still just doesn’t feel right.
- Together: An alternative to Evernote, Together is a pretty classy app. But, at least so far in my experience, the process of getting information into the app is far too tedious, as is the process for properly tagging that information. I may just need to spend more time learning the app, but if something isn’t easy to use then I know from experience that I won’t use it.
- Other Apps: There is also Microsoft OneNote, Scrivener, plain text files with nvALT, DEVONthink, Papers, and probably a few others. Some of these simply don’t appeal to me, and some of them I haven’t yet tried out.
Ulysses (My Pick)
I’ve been using Ulysses for quite a long time, but only as a writing app — not for collecting notes and other tidbits related to research.
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Ulysses is a fantastic app, and it does a great job at simplifying it’s vast complexity. However, I didn’t initially consider it for my researching needs because I didn’t think it had a robust search engine. But, turns out, I was wrong.
Thanks to a new project we’re working on here at The Sweet Setup, I just discovered the Smart Filters in Ulysses, and whoa. These filters are basically smart folders. You can create all sorts of variables for how you want sheets to be filtered, and you can even move the filters around within different groups so as to bring up different results based on the group.
For example, here’s a filter I set up to search within all my book quotes for any notes that contain the keywords “business” and “creativity.”
And here’s a filter I set up that shows me any and all notes I’ve created or worked on within the past 48 hours.
Input and Organization Within Research Apps
The two things that matter most to in my use of notes and research apps are: (1) ease of input and (2) powerful search and categorization. It seems that many apps excel at one or the other, but not both.
It’s also critical that these research apps be full-featured on both Mac and iOS.
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That’s why Ulysses smart filters are so exciting to me. You can get more complex than what I’ve shown above. You can include parameters that search the entire text of a note (not just the keywords/tags), and you can also include “negative” search parameters that exclude notes with certain words. And, these smart filters also sync between Mac and iOS versions.
My biggest quibble with Ulysses right now as a note-taking, researching tool is the way it handles inline images. If the image is inline with a note, you see an
IMG
markdown tag. Or, an image can be attached to a note, but otherwise not shown inline. It’d be great to be able to have images displayed inline.Though, I do like how you can attach images to a note (if you want an image / screenshot nearby as reference material, but perhaps not as something you want to be in-line with your actual text).
So, all that said, I’m obviously now using Ulysses (Mac / iOS) as my writing and researching app of choice, and I’ve already begun transcribing all my book notes and highlights into the app.
And, as I mentioned, we’ve got something brand new related to Ulysses in the works. Click here to find out more.
Stop losing your ideas and notes to multiple apps…
An online course to help you save time, organize your notes, and master the best writing app for Mac and iOS: Ulysses.