EnzymeX by Alexander Griekspoor
and Tom Groothuis
Winner: Best Mac OS X Scientific Computing Solution
Molecular biologist Alexander Griekspoor didn’t set out to become a software developer. He was just trying to find an easier way to do his job.
High-end Multitaskers. Griekspoor and Groothuis developed EnzymeX as well as two other scientific software applications while working toward their PhDs in molecular biology.
Not only did he accomplish this feat, but EnzymeX, the software application Griekspoor created with his friend and colleague, Tom Groothuis, was impressive enough to win top honors at Apple’s 2006 Worldwide Developer’s Conference (WWDC) in the category of Best Scientific Computing Solution for Mac OS X. But equally rewarding to Griekspoor and Groothuis is the satisfaction of knowing that molecular biologists around the world are using EnzymeX to streamline a particularly tedious manual process.
Enzymatic Cut and Paste
Available as freeware exclusively for Macintosh, EnzymeX is used in the creation of DNA constructs, a process by which molecular biologists take apart DNA and test various segments to determine the functions of proteins. To form these constructs, biologists must cut and reassemble strands of DNA in the laboratory using enzymes they purchase from any of about 600 different vendors.
“The Mac OS X tools were what got me started. That’s when I taught myself how to program. I made my first application, Lab Assistant, in six months.”
Functioning like custom-made scissors and glue, the enzymes cut or assemble DNA in specific places, which means that biologists must take care to select exactly the right enzymes to do the job. And further complicating matters, when they use more than one enzyme at a time — for instance, when excising DNA fragments that have different bases or sequences at each end — biologists need to carefully control the laboratory conditions to make sure the enzymes can coexist and still work properly. “All these enzymes have different characeristics,” he explains. “So you have to use them at specific tempreratures, and you have to use them in specific solutions.”
Replacing a Manual System. Before EnzymeX, molecular biologists had to pore through scores of catalogs to find just the right enzymes and the exact conditions for using them. “After we finished the first version of EnzymeX, we threw away a one-meter stockpile of catalogs,” says Griekspoor.
Manual Labor
Until EnzymeX was available, molecular biologists flipped through stacks of manuals and spent hours sorting out this information. First, they had to determine which enzymes could do the specific task and identify the laboratory conditions they’d require. Compounding the problem, says Griekspoor, was the fact that manufacturers often make it difficult to compare enzymes made by competitive companies. “It’s very difficult to cross-compare,” he says. “And this of course may be logical, because they would like you to buy all the enzymes from them only.”
Griekspoor and Groothuis first envisioned EnzymeX as a simple database. Soon afterward, they realized they could develop it to handle the tedious calculations and cross-comparisons. “What we did next was think of a way you could enter, say, Enzyme One from Manufacturer A, and Enzyme Two from Manufacturer B, and it would give you the best conditions you should use,” Griekspoor explains. “This was something you could do with pencil and paper, but it would take a very long time and sometimes was almost impossible.”
A Self-taught Mac Programmer
When he was a student, Griekspoor became interested in developing applications for Macs after Apple released the public beta of Mac OS X. “While I’ve always been a fan of the Mac, I was never a programmer and I don’t have that background,” he says. “When the public beta of Mac OS X came out, it came with all these free development tools you could create programs with. Until then I’d had the interest but never pursued it. But basically, the Mac OS X tools were what got me started. That’s when I taught myself how to program. I made my first application, Lab Assistant, in six months.”
It was an auspicious beginning. In 2004, their second application, 4Peaks, won them their first ADC award, with Griekspoor doing the programming and Groothuis focusing on support and managing their website. Not long afterward, the two started working on EnzymeX.
Evolution Combined With Intelligent Design
With customer input and enthusiastic attention to detail on the part of Griekspoor and Goothuis, EnzymeX continues to evolve. Its current iteration includes a reverse-lookup function, which allows molecular biologists to learn where within a specific DNA sequence any of the 600 enzymes will cut. “Now it’s like a text editor for DNA,” Griekspoor says. And with the introduction of Mac OS X Tiger, he included support for Spotlight. “It offers you a little inspector that automatically finds all the Enzyme X files, all the DNA files on your Mac,” he explains. “And then you can double-click and open them without having to look for where they are on your hard disk.”
When Griekspoor and Groothuis finish their PhDs in Amsterdam in November, Groothuis plans to continue working in biology, but Griekspoor has other plans — which include a dramatic career change. “This got so much out of hand that I realize I like to do this more than the real wet lab biology,” he says. “I will completely change fields. I will go to the European Bioinformatics Institute in Cambridge, U.K., to work on providing more tools to researchers. It’s exciting, I think.”
