BU-Wellesley Software, a multidisciplinary research team comprised largely of undergraduates from Boston University’s College of Engineering and Wellesley College focused on challenges in synthetic biology, edged out teams from the U.S., Europe and Asia to win in the “Best Software Tool” category at the International Genetically Engineered Machine (iGEM) World Jamboree at MIT. The team earlier won a gold medal for their overall performance at the iGEM Americas Regional Jamboree in Indianapolis.
“They did great,” said Assistant Professor Douglas Densmore (ECE), who co-organized the team with Wellesley College Computer Science Assistant Professor Orit Shaer. “We had a large team of 19 students and six advisors spread over the two campuses, and the collaboration went very well.”
In addition to BU and Wellesley College, the team included members from Olin College; Suffolk University; University of California, Berkeley; Framingham High School; and Tufts University. This year’s iGEM competition was Boston University’s first since 2006, though Densmore had competed previously with UC Berkeley in 2008 and 2009.
Taking on TB
Drawing more than 160 teams and 2000 participants from 30 countries this year, and supported by 14 industrial and government sponsors, the eight-year-old iGEM competition is the premiere undergraduate synthetic biology competition. Each team spends one summer developing simple biological systems from standard, interchangeable parts and operating them in living cells, with an eye toward advancing solutions to healthcare, energy and other critical societal problems.
For their project BU-Wellesley Software designed a collection of five software tools to support a joint BU-Wellesley College research collaboration focused on better understanding the bacterium that causes tuberculosis, a lung disease that infects one-third of the world’s population and causes up to three million deaths each year. Built using Densmore’s Clotho synthetic biology software platform, the team’s highly collaborative synthetic biology tools could help accelerate BU-Wellesley efforts to systematically assemble specific DNA sequences used to model “circuits” of gene interactions within the regulatory networks of the bacterium—information that could lead to more effective diagnostics and drugs for TB.
“Our software lets you make a reconfigurable DNA circuit—producing it once and reconfiguring it for multiple experiments, either in computer simulations or in the lab,” said Densmore. “By isolating genes suspected of transforming the TB bacterium to a pathogenic state and studying their interactions, we hope to better understand this process and how to inhibit it.”
A Fruitful Collaboration
Led by Densmore, ECE postdoctoral research associates Swapnil Bhatia and Traci Haddock, and BME graduate student Suma Jaini, the team’s BU-based members developed automated design software for configuring sequences of DNA that take specific biological building blocks and assemble them automatically using liquid-handling robots in the laboratory environment. Guided by Shaer, the Wellesley team members utilized advances in computer-human interaction such as interactive surfaces, multi-touch and gesture-based interaction to enhance collaboration and productivity in synthetic biological teams.
“Advances in human-computer interaction offer natural, intuitive and collaborative ways to operate computational systems,” said Shaer. “In the context of synthetic biology, reducing the mental workload required to process vast amounts of information and supporting collaborative work could lead to new scientific discoveries.”
“This is a terrific chance to examine a real application with tremendous potential benefits to world health,” said Densmore. “Our ability to clearly demonstrate computer software’s capacity to explore the systematic assembly of novel networks to investigate TB will have a dramatic effect on our ability to design biology in general.”
For teammate Craig LaBoda (ECE ’11), a 2010 Lutchen Fellow who is now an electrical engineering PhD student at Duke University, working with students from Wellesley College was a real plus.
“From our collaborators at Wellesley College who specialize in human-computer interaction, I’ve learned a great deal about the user-centered software design process,” said LaBoda, who this summer helped develop one of the team’s five software tools, Trumpet, which enables synthetic biologists to design completely configurable genetic circuits. “This helped us tailor our synthetic biology software for end-users through feedback at different stages in the design process.”
For Alberto Purwada (BME’13), who received STARS funding to participate in the BU-Wellesley iGEM team, the project served to demonstrate the relevance of introductory engineering courses.
“As a biomedical engineering student, I’ve been taking core engineering classes,” he said. “I wanted to start to see how we could use this knowledge to solve a problem in biology or medicine, and iGEM has been a great way to do this.”