As busy, full-time researchers at The Netherlands Cancer Institute, Alexander Griekspoor and Tom Groothuis needed an application to organize their research papers. They envisioned a program that could search various databases as well as download, import, read, organize, store, and share PDF-based research papers. Griekspoor and Groothuis believed they could create such an application, which didn’t then exist, but they didn’t have a lot of extra time to work on its development.

Already experienced Mac OS X developers (their other products include EnzymeX and 4Peaks, both Apple Design Award winners), Griekspoor and Groothuis knew that they wanted to use Xcode and the Mac OS X frameworks to develop their application, Papers. They didn’t have time to fool around with anything less complete. By using the most advanced Mac OS X tools, they were able to save development time while creating a powerful yet easy-to-use application that has been a hit in the scientific community.

Organizing Research with Papers

Griekspoor describes Papers as a kind of “iTunes for PDFs.”

He says, “Replace MP3s with PDFs, and you have Papers. Before Papers, you had to download your documents from the web, store them on your hard disk, and develop your own way of renaming and organizing. This is almost an undoable job.”

Not only does Papers solve the problem of organizing PDF files, it does much more. Papers lets users search the PubMed database, a free search engine that offers access to MedLine, which archives international research in the life sciences and biomedical fields. Searches are launched right from Papers, and the results return not only research papers but also the metadata essential to organizing a personal research library-data such as author, title, and journal.

The application also provides an address book-like feature that organizes author contact information, as well as drag-and-drop functionality that imports and organizes existing PDF files. Papers supports Collections, essentially groups of research articles arranged in folders. Users can also create Smart Collections, which automatically group articles according to information included in the metadata. Finally, Papers supports export to BibTex, Bookends, Endnote XML, and RIS.

“It’s really one program that captures the whole workflow of dealing with scientific literature,” Alex says. “I like a desktop application that is fully integrated with the Mac operating system; it enables a workflow that interacts with your web browser, address book, and other applications..”

And how have their users responded?

“The feedback has been enormous;” Alex says, “It shows there clearly was a need for such a program.”

A Natural Evolution to Mac OS X Development

Griekspoor has been a Macintosh user since the age of 10, and offers reasons why the Macintosh platform makes the most sense for his development efforts.

“It’s my platform of choice,” he says. “In the biology and science communities, in general, Macintosh is pretty popular. With my background in biology, I know what I would want to use and how I would like to build it. I don’t have any background in IT or computer programming, but I believe the Mac is the only platform where I could have done all of this.

For many developers, a key strength of the Macintosh platform is that it stays out of their way, and empowers them to pay attention to the actual tasks they want to accomplish, rather than spend time learning the complexities of software development.

”The nice thing about the development environment is that you can focus on what makes your application special,” says Alex. “I know what people would like to see, and I don’t have to focus on the technical details because for the most part they’re handled by what Apple provides. That’s the great part of the Mac OS X frameworks.”

Leveraging Mac OS X Technologies

Alex and Tom had a three-month period during the summer during which they could dedicate their time solely to developing Papers. Because they had limited time and resources, they relied on a host of Mac OS X technologies, including Core Data to support the Papers database, WebKit to automate downloading PDF files and integrated online help, PDF Kit to display PDF files, NSXML for parsing PubMed queries, Spotlight and NSPredicate for local database queries, and AppleScript for email integration. These technologies provided the essential foundations for building Papers.

The problem of organizing his research papers is one that had bothered Griekspoor for quite some time. But it wasn’t until the 2004 Apple Worldwide Developers Conference (WWDC), when new Mac OS X Tiger technologies such as Core Data and PDFKit were introduced, that he realized his vision for a reference research tool was in reach.

Griekspoor says, “A number of new technologies in Tiger were introduced, especially PDFKit, which provide all the functionality of Preview without programming; Core Data, which lets you store all this metadata; and Spotlight, which lets you search all this stuff. Apple introduced all of these technologies in a row, and for me it was a light bulb going on—all of these components, mix them together, and you have something like Papers.”

Papers Extensibility

To help support the continued evolution of Papers, Griekspoor and Groothuis recently introduced a plug-in software development kit (SDK). It allows other developers to provide extensions to Papers’ import and export mechanisms. In addition, the plug-in SDK has enabled Griekspoor to build the interfaces for the new search engines that are being integrated into Papers.

Providing extensibility to their applications for developers is nothing new; the team’s other major applications, 4Peaks (which won an Apple Design Award in 2005 for Best Student Product) and EnzymeX (which won Best Scientific Application in 2006), also provided plug-in SDKs. The Papers SDK contains everything a developer needs to get started, including documentation, sample code, and a test application.

Building a Community

Although building an application like Papers is an impressive feat in and of itself, Griekspoor and Groothuis have also successfully developed a community around Papers. Because they’re such a small development team, additional help to support Papers isn’t readily available. With WebKit, however, support is built right in.

“It’s difficult for a single person to support such a program,” Alex explains. “We came up with the idea of integrating the Papers website into the program, and WebKit allows you to do this. We can support Papers without the need for five additional people.”

Thanks to WebKit, Papers is building a scientific social network, with user forums integrated into the application.

Alex says, “In general, Mac users readily form communities where they help each other. In a short time, 750 people joined the Papers forum and contributed. In the future, we hope to be able to create real scientific communities, with much more interaction capabilities aimed at science.”

Papers also integrates extensive help files and videos to help users get started. Groothuis is responsible for the website, development of the help files, and the tutorial videos.

Looking Forward to Leopard

The release of Mac OS X Leopard is exciting for Griekspoor, who is responsible for the primary development of the software. Their planned Leopard release will be focused on integrating the new Leopard frameworks and features, such as PDFKit and Core Data. Some of the new Papers features will reference management functionality, include interaction with Microsoft Word and other text editors, and add the ability to highlight and annotate PDFs.

Alex expects the new features in Xcode 3.0 and Objective-C 2.0 to have the biggest effect.

“We are very excited about Leopard," he says. “Apple is providing a number of new frameworks and functionality. The changes to Objective-C 2.0 get rid of all the memory management, which can be quite a pain; this will help us to eliminate a third of our code. We see the core frameworks as more stable and reliable.

“Core Data can be seen as a version 2.0 product now that it has been further improved in Leopard—it is much faster. In addition to that, we get all these other technologies that are great to build into Papers, such as the highlighting and annotations built into the new version of PDFKit.”

Moving Beyond Biomedical Research

Although the integrated search engine in Papers is currently focused on PubMed, Griekspoor and Groothuis aren’t content to stop there. They have plans to broaden their application’s reach to other research disciplines that have the same fundamental needs as the biosciences.

“We used our expertise in the biomedical field to build the application,” Griekspoor explains. “But there have been a lot of requests for integration with other search engines beyond PubMed. We want to provide a platform where all search engines work the same.”

The next release of Papers will extend its unified search interface to work with Google Scholar, CiteSeer for computer science researchers, arXiv for physics and mathematics, Web of Science for general science, and Scopus-the largest research citation database.

Looking to the Future

Griekspoor and Groothuis have achieved a lot during the past few years: winning their third Apple Design Award for Best Scientific Application for Papers, earning their PhDs, developing numerous scientific applications, and much more.

“This all started out as a hobby in 2000, but now the official Mekentosj company has been started [in mid-September 2007],” Griekspoor says. “Starting in November I’ll be working full time at this. It shows how this can grow, and it can really lead to something you can do full time. I have so many ideas that the program can be expanded with, and hopefully from November forward I can fully focus on that.”

The scientific and research communities will be looking to Mekentosj as it continues to blaze trails in developing the Mac OS X applications they want and need.

For more information about Papers, see the Mekentosj website.