Good software solves a problem. When one journal after another switched to PDF as electronic document format, and journals started to appear only in electronic form, storing papers as printouts in folders became impractical. But the PDF files will soon start to clutter the hard drive, despite efforts to organize them by topic, year or author. At least for Macintosh users, Papers (https://web.archive.org/web/20150924053037/http://mekentosj.com/papers/?) is one practical and elegant solution to this problem. I talked with Papers author Alexander Griekspoor (https://web.archive.org/web/20150924053037/http://network.nature.com/people/mekentosj/profile?) not only about Papers, but also about his career switch from cell biologist to software developer.
The tag-line we coined for Papers is “your personal library of science”, a play-of-words on the well-known PLoS acronym. And this program for the Mac provides exactly that, it helps you manage and organize your personal scientific literature library. It provides a complete workflow for finding new articles using built-in search engines, browsing the publisher’s website using the built-in Safari web browser, downloading, archiving and renaming the PDF files, and organizing and indexing these articles. Finally, it allows you to easily read the papers and share them with colleagues.
Papers distinguishes itself from other bibliography tools in that it is not a typical reference manager to begin with. The Mac has had several good reference management applications for a long time already, but when I created Papers I wanted to make a different application, one that didn’t exist yet and one there was clearly a need for, one to manage all those PDF files that people were downloading. In the years before, the publishing industry had introduced PDFs as a replacement for sending articles by regular mail and it was a great success in that it made access to the literature much easier.
Still, their support of the researcher ended the moment you pressed the download button. Your web browser would save some cryptically named PDF file on your hard disk, which soon quickly filled up with dozens of these files. So whereas PDFs were introduced to save us from the messy file cabinets with hundreds of paper copies of your articles, we were now facing the digital equivalent of that on our desktop.
That was when it struck me that Apple had already solved this issue for MP3 files a few years earlier, iTunes had allowed us to stop bothering about managing MP3s and instead allowed us to focus on the songs. Papers was designed to do exactly the same when it comes to managing PDFs and instead lets us focus on the articles. Obviously, now the have seen how things can be different you notice that most reference managers on the Mac have started to play catch up, and are introducing PDF management features as well. Still, for us this has always been the key element and is just the start of many exciting things to come.
The most obvious answer is to buy a Mac of course 😉 But more seriously, at the moment I’m not aware of a program on Windows or Linux that offers the same feature set and user experience that Papers offers. But like the other reference management tools on the Mac there’s a similar trend of adopting
these kind of features in bibliography tools on Linux and Windows as well.
Perhaps surprisingly I’m a cell biologist of training and not a computer scientists or IT person. I studied medical biology at the Free University in Amsterdam and ended up doing my PhD at the Netherlands Cancer Institute in Amsterdam as well, where I studied the immune system using live-cell fluorescence microscopy (https://web.archive.org/web/20150924053037/http://dx.doi.org/10.1016/j.mib.2005.04.007?).
It all started out as a hobby driven by a long-time interest for both design and technology. I was introduced to the Mac when my dad brought home one of these “portable” classic Macs when I was about 14 years old, and almost immediately I started experimenting with Photoshop et al. During university I earned some money in my spare time by designing and building websites, but it wasn’t until about the time I started by PhD that Apple introduced Mac OS X and with it came the free set of developer tools that finally made it easy enough for someone without the classical IT background to start building his/her own Mac applications. Together with my best friend and fellow PhD student Tom Groothuis we started building a number of tools for molecular biologists (EnzymeX (https://web.archive.org/web/20150924053037/http://mekentosj.com/enzymex/?)), which we distributed for free under our “mek en tosj” monicker. It didn’t take long before the hobby started to get out of hand as the popularity of our programs started to soar.
When the time came to pick a postdoc I knew one thing for sure, the programming was something I was so passionate about that it should be part of the postdoc rather than a spare time project. That’s why I picked the text mining group at the European Bioinformatics Institute (https://web.archive.org/web/20150924053037/http://www.ebi.ac.uk/?) in Cambridge UK, also driven by an interest in the changes that were/are ongoing in the scientific publishing industry. I applied for a two year EU Marie Curie fellowship which I was fortunate to get, however it would take a few months between the end of my PhD and all the bureaucracy before I could get started in Cambridge. This was when I decided to build Papers. I got the idea for this “iTunes for PDF files” already two years earlier, but never had the time to do it. I did tell everybody I knew about it, but no one had done it and now finally I had some spare time on my hands.
The first beta of the program was released right at the time I started my postdoc and it was a success right from the start. In fact it was so successful and offered so many opportunities that it was soon difficult to focus on my actual postdoc and after a year I realized that this was the thing I was really passionate about and was what I wanted to concentrate fully on. That was when I decided to quit my job and become the company founder of Mekentosj Inc. 😉
It’s still to early to talk in many details but like I said, for us the current version of Papers has always been the foundation on which we can build many exciting things we envision. We’re working hard on the next major release of Papers which will definitely be a big step up. And obviously the introduction of the iPhone is something that also brings very exciting possibilities, so many things to look forward to!
Alex, thanks a lot for this interview. For more information, you can read an interview (https://web.archive.org/web/20150924053037/http://www.macresearch.org/interview_with_alexander_griekspoor_from_mekentosj?) from two years ago, or visit the Mekentosj Papers Nature Network Forum (https://web.archive.org/web/20150924053037/http://network.nature.com/groups/papers/forum/topics?). And please tell me how you manage all these PDF files and how you use these references when writing a paper yourself.