Interview with Alexander Griekspoor

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 is one practical and elegant solution to this problem. I talked with Papers author Alexander Griekspoor not only about Papers, but also about his career switch from cell biologist to software developer.

1. Can you describe what Papers is and does?
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 organise 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 PDFfiles, and organising and indexing these articles. Finally, it allows you to easily read the papers and share them with colleagues.

2. How is Papers different from other Macintosh bibliography tools?
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.

3. What recommendations do you give Windows and Linux users?
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.

4. What did you do before working on Papers?
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.

5. How did you get involved in writing Macintosh software?
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), 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.

6. You talked about your postdoc choice in a 2007 Nature Jobs article. What made you decide to move from postdoc to company founder?
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 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 realised 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. 😉

7. Do you want to talk about future plans for Papers?
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 from two years ago, or visit the Mekentosj Papers Nature Network Forum. And please tell me how you manage all these PDF files and how you use these references when writing a paper yourself.

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14 Responses to Interview with Alexander Griekspoor

  1. Stephen Curry says:

    Great interview Martin. I managed to bump into Alexander at “SciBlog08″: (well in the pub afterwards) with the sole intention of telling him how great _Papers_ is. He was one of those friendly “strangers”: that I was going on about the other day. The program works beautifully – it makes organisation and retrieval of pdfs a snap. I have started to explore “Mendeley”: a bit but it will take something really great to prise me away from _Papers_.

  2. Martin Fenner says:

    Thank Alex for the interview ;). For me Papers is _almost_ perfect. My two wishes for the next version:
    *Integration with Microsoft Word*. I currently export to Endnote when writing a paper. Papers also exports to the new Microsoft Word 2007/2008 bibliography format, but that format only supports a few journal styles, none of them really helpful for scientists.
    *Online sharing of references*. The new Archive function is a great way to share references with others, but it’s still very different from what you can do with Connotea, CiteULike and the like.

  3. Stephen Curry says:

    Hear, hear for Word integration. But I still haven’t figured out online reference tools like Connotea – do you make a lot of use of it – or Mendeley?

  4. Maxine Clarke says:

    How about a PC version?

  5. Martin Fenner says:

    I use Connotea, but it is not really part of my workflow when working on a paper or keeping up to date with the literature in my field. Mendeley is still too new to tell. I have in mind what Eva said in a “recent blog post”: I want to continue using Papers, as it is a great tool. But it would be great if there was some Web 2.0 functionality that expands the usefulness by sharing your reference lists with others.

  6. Richard P. Grant says:

    bq. _How about a PC version?_

  7. Martin Fenner says:

    One reason I have to use Endnote when writing a paper is that usually at least some one coauthor uses Windows. That would be a problem for a Papers Microsoft Word plugin, and is also one big reason I didn’t swith to “Sente”: a few years ago. Mendeley is unusual in that the desktop version is available for Windows, Mac and Linux.

  8. Maxine Clarke says:

    You may laugh, but I don’t see why using a PC is so derided. A heck of a lot of scientists and others use them, so why shouldn’t a service, in principle, be usable on it? (eg Google takes care of this.) I imagine that Alexander would appreciate that it is not a very useful business response to mock someone’s working tools.

  9. Philipp Selenko says:

    I love papers! And I make all people in my lab use it. One disadvantage though > we (as a lab) cannot SHARE a central library and then add our individual pdf’s. Kind of like weTunes rather than iTunes for pdfs.

  10. Richard P. Grant says:

    Maxine, it’s refreshing to see people who use Windows (not PCs) ask for software that’s Mac only. Makes Oi larf, it does (especially when you get morons—not including present company, obvious—saying “I don’t use a Mac because there’s no software for it”).
    Oh, and iWork? I’ve had people asking if there’s a Windows version because they like mine so much.

  11. Alexander Griekspoor says:

    @stephen: Thanks Stephen, great to hear you like the program so much and it’s always very nice to meet people in real life who use our programs!
    @martin: You’re welcome, thanks for having me on your blog! Word integration (reference management in general) and sharing (also @Philipp) are two of the most requested features we get, along with the ability to annotate your PDFs, you bet we’re looking into that!
    @maxime; You are right there are tons of researchers using a PC and they’d love to use Papers (believe me we get plenty of emails confirming that). My answer has always been that as a small company we have to focus on what we do best. Papers is all about user experience and our expertise is clearly Mac oriented. In addition the choice between having to personally do the same thing again or doing really innovative things is an easy one. I’ve learned to never say never though.

  12. Maxine Clarke says:

    Richard – since I’ve been using the internet, and particuarly since using blogs and other interactive tools, I’ve seen tens or maybe even a hundred or two, applications I would like to try out but they are Mac-only.
    I work in a predominantly PC-based office – the people who use Macs are almost all the production and design staff – because the software available for Macs is more suited to what they do than PCs.
    So I don’t get your point. Never mind, though, it isn’t a big issue.
    Alexander – thanks. I appreciate your reasoning, I was just making the point that I did not think you would “laugh” at someone asking for a service you had not developed- I imagined your reply would be along the lines that it, in fact, was! Glad that your Papers product is working out so well.

  13. Martin Fenner says:

    Part of the fun using Papers is the elegant user interface and clever use of Apple technologies, and not surprisingly it has won a “Apple Design Award 2007″: for best scientific computing solution.
    The Nature News article from April (“Programs promise to end PDF paper-chase”: and the comments to that article not only discuss Papers, but also mention some other programs:
    * “iPapers”: (Mac)
    * “gPapers”: (Linux)
    * “Bookends”: (Mac)
    * “Zotero”: (Firefox plugin, Windows, Linux, Mac)
    * “A.nnotate”: (Web-based)
    * “Google Desktop”: (Windows, Linux, Mac)
    * “EasyArticles”: (Windows)
    * “Adobe Digital Editions”: (Mac, Windows)
    Zotero is the most popular of those. The upcoming version 1.5 will allow online access to your Zotero library (“Browse your Zotero Library Online”:, including a special iPhone-formatted version. And Alex also mentioned the iPhone in his answer to my question about the future of Papers…

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