ICB3 announces Open Source Software Innovation (OSSI) Competition awards

Nov 06 2013

The Institute for Computational Biology, Biostatistics, and Bioinformatics (ICB3) is pleased to announce the results of its 2013 Open Source Software Innovation (OSSI) competition. Two entries received top prizes of $4,500:

  • Hardware and software for single-molecule fluorescence analysis” won for Best Integrated Software System. Benjamin Gamari (graduate student, physics) led the team, which included Laura Dietz (postdoctoral research fellow, computer science), and Lori Goldner (professor, physics).
  • Mixed modeling of meta-analysis p-values (MixMAP)” project by Gregory Matthews (lecturer, biostatistics) won the prize for Best Emerging Software System.

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

  • mCrowd:Data Collection and Visualization,” Siddharth Gupta (team leader, graduate student, computer science), Abhinav Parate (graduate student, computer science), Moaj Musthag (graduate student, computer science) Deepak Ganesan (associate professor, 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 interval-censored survival data,” Nicholas Reich (assistant professor, Biostatistics)
  • Website to estimate energy expenditure from accelerometer data and WebDevelopR,” Evan Ray (team leader, graduate student, mathematics/statistics), Peter Krafft (computer science & artificial intelligence laboratory, Massachusetts Institute of Technology), John Staudenmeyer (associate professor, mathematics/statistics)
  • Genome Hash: A program that scans genomes for clusters of user-defined sequence motifs,” Michelle Markstein (team leader, assistant professor, biology), Peter Markstein (Life Sciences Society), Vicky Markstein (Life Sciences Society)

Associate Professor of Computer Science David Jensen coordinated the competition and observed, "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 trans-disciplinary 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; Coordinator, Statistics Program, Mathematics & Statistics
  • Jonathan French, Principal Scientist II and Director of Innovation, Metrum Research Group
  • Burnley Jaklevic, Senior Licensing Officer, Office of Commercial Ventures & Intellectual Property
  • D. Joseph Jerry, Professor, Veterinary & Animal Sciences
  • David Kulp, Research Scientist, Fiksu, Inc.
  • Keith Parent, Chief Executive Officer, Court Square Group; Vice President Engineering, EmpiraMed, Inc.

The ICB3 team is very appreciative of the judges for their time and thoughtful efforts. The mixture of on-campus and industry-based judges was intended to provide broad perspective. Keith Parent says, "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 cross roads 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 November 15, 11:45 to 2:30, in the Marriott Center on the 11th floor of the UMass Amherst Campus Center. For more information about ICB3 and to register for the annual meeting, visit http://www.umass.edu/icb3/