NSF Awards Densmore $1.1M for Clotho Research

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Clotho presents a set of modular Apps for the specification, design, and assembly of novel biological systems. Apps are included with the software or can be written by the larger community.
Clotho presents a set of modular Apps for the specification, design, and assembly of novel biological systems. Apps are included with the software or can be written by the larger community.

In 2007, Assistant Professor Douglas Densmore (ECE) and his research team at the University of California, Berkeley started working on software that could engineer synthetic biological systems and improve how the data behind them was managed. Their work had the potential to improve disease diagnosis and treatment.

Five years later, their research is still going strong. Densmore was recently awarded a three-year grant totaling $1.1 million from the National Science Foundation’s Advances in Biological Informatics (ABI) for his open source platform, better known as Clotho.

“We’re very excited to work with NSF to take Clotho to the next level,” said Densmore. “This will start paving the way for Clotho to go from a proof of concept to viable commercial software.”

The project includes collaborations with researchers at Boston University, UC Berkeley, the University of Washington, and BIOFAB. Professor J. Christopher Anderson of UC Berkeley is a co-principal investigator on the grant and a co-founder of the Clotho framework.

Clotho helps manage complex DNA assembly processes by capturing the biological protocols formally and also providing commands to liquid handling robotics for their physical assembly and sample tracking.
Clotho helps manage complex DNA assembly processes by capturing the biological protocols formally and also providing commands to liquid handling robotics for their physical assembly and sample tracking.

Clotho uses an App environment similar to an iPhone so that anyone can share and create new tools. At the same time, it provides a mechanism to begin the process of creating standardized data, algorithms, and methodologies for synthetic biology.

The grant will provide Densmore and his research team with funding that will allow them to complete the development of the software. Their App store will serve as both a portal for Clotho development and a community resource.

Earlier this year, Clotho also acted as an educational resource by providing students with a chance to develop their own automated design software. Using Densmore’s platform, a team made up of Boston University and Wellesley College students used Clotho to create software tools that could potentially lead to more effective diagnostics and drugs for tuberculosis. They went on to win the “Best Software Tool” prize at the International Genetically Engineered Machine (iGEM) World Jamboree at MIT.

-Rachel Harrington (rachelah@bu.edu)

Related links:
“Densmore Research Website Honored by the Communicator Awards”
“BU-Wellesley Team Wins ‘Best Software Tool’ Award at iGEM World Jamboree”
“BU-Wellesley Software Wins Gold at iGEM Americas Regional Jamboree”