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HHMI Fellow's "Webcutter" Site Cuts Through the Grind

HHMI Fellow's "Webcutter" Site Cuts Through the Grind

Summary

HHMI predoctoral fellow develops a computer program that offers a quick, easy and free way to produce restriction maps of DNA sequences.

Max Heiman, a Yale undergraduate doing research in the laboratory of Massachusetts General Hospital scientist Steven Reeves, had a problem. He and coworkers were determining which sites on the DNA sequences they were studying would be cleaved by restriction enzymes. But the computer program they were using to map the restriction sites was inconvenient and sluggish.

Heiman knew he could write a better programso he did. The result is Webcutter, a site on the World Wide Web that for the past two years has offered a quick, easy and free way to produce restriction maps of DNA sequences (http://www.ccsi.com/firstmarket/cutter) . "It's gotten a great response," Heiman said. "Thirty people used it the very first day, and from the e-mail I've been getting it seems that even more people are using it now."

Now a Hughes predoctoral fellow at the University of California, San Francisco, Heiman considers himself a biologist, not a computer programmer. However, as he considers the prospects of a commercial version of Webcutter, he is looking forward to adding "entrepreneur" to an already crowded resume. "I've always been really happy that people were using it," he said, "and the possibility that I could make a little money off it is amazing."

Heiman learned about computers by playing with them when he was young. The personal Web page he constructed while at Yale still offers links to several of his favorite games (http://pantheon.yale.edu/~maxwell). The same informal approach led to the creation of Webcutter. Before going to work with Reeves at Massachusetts General, Heiman helped set up a Web site for his father's marketing research firm. In the process, he learned Perl, a computer language that can search long blocks of text. When he encountered the problem with restriction enzyme mapping, Heiman realized that Perl could be used to match the As, Ts, Gs and Cs of DNA sequences.

"He came here to do basic biological research," said Reeves, whose lab continues to use Webcutter today. "The computer program was something he developed between incubating tubes. He'd walk over to the Mac and start playing with the program. He's a very motivated student."

Several commercial software packages that can map restrictions sites are currently available on CD-ROMs and floppy disks. Web-based alternatives to these commercial programs are becoming common, notes geneticist George Church of Harvard Medical School whose laboratory was one of the first to share functional genomics projects on the World Wide Web. Many of these sites are being developed and maintained by undergraduates and graduate students in the sciences. "Computer applications in biology have always presented projects that undergraduates could tackle," said Church, "and do so with lots of energy and fresh viewpoints."

In the past, computer programs developed by students might be used within a single laboratory or campus. Now, the World Wide Web has made everyone a potential publisher with a worldwide audience. Webcutter already has a mirror site in Sweden, and Heiman has talked with other biologists who want to set up sites elsewhere.

Commercial software developers are paying close attention to this trend and lining up possible products to offer online. Already, Heiman has been working on a version of Webcutter that will be incorporated into a product scheduled for release next year. Carolina Biological Supply Company is putting together an educational kit for high school biology teachers that is organized around Webcutter. "We decided to go with Webcutter because we can provide it at much lower cost and because so many classrooms already have net access," said Maria Rapoza, a senior scientist at Carolina Biological Supply. "Even if a network connection is just in the school, students can use it during their study break, or they can use their computers at home."

Webcutter is not Heiman's only Web-based interest. While at Yale, he also put together a database that undergraduates can use to look for research projects. Again, the idea grew out of a problem. "I didn't want to stay in New Haven over the summer, but I didn't know anyone anywhere else. So I went to all these university Web sites, looked at the research pages, and mailed the PIs. That's how I got my job with Massachusetts General."

Heiman realized there was no reason for other undergraduates to repeat the work he'd done. "I thought it would be nice to have a central database of labs that are undergraduate-friendly and have the resources to train undergraduates from other parts of the country." Heiman created Fitzroy, an online gathering place where undergraduates could post descriptions of their research jobs and read about the experiences of others (http://www.firstmarket.com/fitzroy). The site, which Heiman no longer has time to update, offered "a way for undergraduates to network among themselves," he said.

Although Webcutter is moving into the commercial world, Heiman doesn't want to leave his roots behind. So long as he can find servers willing to host it, he plans to leave the existing version of Webcutter online and free. "Biology labs have given me a lot," he said, "and I'm glad to give something back."

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Jim Keeley
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