posted January 23, 2012

Computer Science Students Publish Software in Use around the World

From left to right, Josh Kammeraad, Nick Hazekamp and Ben Bockstege.

Three Hope College computer science students have published bioinformatics software that is now in use by scientists around the world.

Working together with Professor Matt DeJongh during the Summer 2011 on-campus research program, sophomore Josh Kammeraad of Bethel Park, Pa., junior Nick Hazekamp of Janesville, Wis., and 2011 graduate Ben Bockstege (who is now pursuing a doctorate in computer science at the University of Notre Dame), completed the first version of the CytoSEED software package that enables viewing, manipulating and analyzing metabolic models created using the Model SEED.

The release of CytoSEED represents the culmination of three years of work by Professor DeJongh, more than a dozen computer science students, and one local high school student. CytoSEED is released for free on SourceForge.net, and has been downloaded hundreds of times since the end of the summer.

In addition, DeJongh and the students have published a paper on CytoSEED that has recently appeared in the journal “Bioinformatics.”  Also co-authors of the paper are 2010 graduate Paul Frybarger of Darien, Ill., who works at Argonne National Laboratory, and Travis McGeehan, a senior at Zeeland East who participated in summer research at Hope through the college’s REACH (Research Experiences Across Cultures at Hope) program.  In April, DeJongh, Hazekamp and Kammeraad will present their research during the annual meeting of the American Society for Biochemistry and Molecular Biology (ASBMB), being held in San Diego, Calif.

The development of CytoSEED was funded by grants from the National Science Foundation, and its ongoing support and development is funded by the Department of Energy’s Systems Biology Knowledgebase project.