ICB3 Open Source Software Innovation Competition Winners Named

November 8, 2013

The Institute for Computational Biology, Biostatistics, and Bioinformatics (ICB3) has awarded two top prizes of $4,500 in its 2013 Open Source Software Innovation competition.

“Hardware and software for singlemolecule fluorescence analysis” won for Best Integrated Software System. Physics graduate student Benjamin Gamari led the team, which included Laura Dietz, a postdoctoral research fellow in computer science, and Lori Goldner, professor of physics.

The “Mixed modeling of metaanalysis pvalues MixMAP” project by Gregory Matthews, lecturer in biostatistics, won the prize for Best Emerging Software System.

In addition to the top prizes, five entries received honorable mentions:

The project, “mCrowd: Data Collection and Visualization,” was led by Siddharth Gupta, a graduate student in computer science. Team members are Abhinav Parate and Moaj Musthag, graduate students in computer science, and Deepak Ganesan, associate professor of computer science.

“Stratified Weibull Regression Model for Interval Censored Data,” Xiangdong Gu team leader, graduate student, biostatistics, Raji Balasubramanian, assistant professor, biostatistics

“Using coarseDataTools to fit intervalcensored survival data,” Nicholas Reich, assistant professor, biostatistics.

“Website to estimate energy expenditure from accelerometer data and WebDevelopR,” Evan Ray, team leader, graduate student in mathematics andstatistics, Peter Krafft, computer science and artificial intelligence laboratory, Massachusetts Institute of Technology, John Staudenmeyer, associate professor, mathematics and statistics.

“Genome Hash: A program that scans genomes for clusters of userdefined sequence motifs,” Michelle Markstein, team leader, assistant professor, biology, Peter Markstein and Vicky Markstein, Life Sciences Society.

Associate professor of computer science David Jensen, who coordinated the competition, said, “The OSSI competition is an exciting new mechanism to stimulate the development and dissemination of innovative software tools that play an important role in enabling new life science and biomedical discoveries.”

ICB3 director and head of Biostatistics Andrea Foulkes added, “The OSSI competition is a novel initiative to catalyze transdisciplinary research on campus around the mutual goal of developing and disseminating open source software tools. I am very pleased that the judges decided to recognize the accomplishments of teams spanning five different departments for a remarkably diverse body of work.”

The judges for the 2013 competition were Erin Conlon, associate professor and coordinator, statistics program, mathematics and statistics; Jonathan French, principal scientist ii and director of innovation, Metrum Research Group; Burnley Jaklevic, senior licensing officer, Office of Commercial Ventures and Intellectual Property; D. Joseph Jerry, professor, veterinary and animal sciences; David Kulp, research scientist, Fiksu, Inc., and Keith Parent, chief executive officer, Court Square Group; vice president engineering, EmpiraMed, Inc.

The mixture of on-campus and industry-based judges was intended to provide broad perspective. Parent said, “I was extremely impressed with the variety of applicants and could immediately see that I could connect a number of the researchers with some industry partners that I've been working with for years. What a great way to get the word out that UMass Amherst is at the crossroads of both information technology and the life sciences.”

The top teams will each give a short presentation on their winning software tools as part of the ICB3’s annual meeting on Friday, Nov. 15, 11:45 a.m. to 2:30 p.m., in the Marriott Center on the 11th floor of the Campus Center.

 

 

 

 

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