The goal of our research program is to develop the foundational understanding and technologies that will allow us to routinely build large numbers of useful biological systems from standard interchangeable parts. Our specific aims are:

• to develop a conceptual framework for designing small biological components (parts) that can be assembled into devices that will perform a well-characterized function under specified conditions,
• to develop a small number of chassis (assembly substrate and power supply) to host the engineered devices and to assemble several devices as “systems” that accomplish a larger objective or goal (testbeds),
• to develop a set of standards for the interactions of the parts and devices so that the devices can be built more readily and reproducibly (enabling composition),
• to offer the parts, devices, and chassis as open source to other researchers and companies involved in SynBERC, and
• to link these engineering goals within a comprehensive human practices framework.

In addition to the research thrusts and testbeds highlighted above, SynBERC has developed a core of cross-cutting research that provides foundational tools and technologies needed to advance synthetic biology internally and externally. Cross-cutting projects currently include automated DNA construction, models and design, safety and security, and registries and repositories.

 

Parts
Leader: Tanja Kortemme
SynBERC will computationally design and construct cellular “parts” that can be assembled into “devices” (Thrust 2). We define “parts” to be any genetically encoded, basic biological function (e.g., a ribosome binding site, transcription termin-ator, or phosphorylation motif). A key component in the “parts thrust” is developing a framework for parts design that takes into account part function, and part-part interactions. More->

Devices
Leader: Christopher Voigt
We will assemble cellular “parts” into “devices” that can be reused in a combination of “systems.”  Here, “devices” are defined to be collections of parts that perform one or more human-specified functions under defined con­ditions (e.g., a Boolean logic oper­ation, a feedback control loop, or a chemical transfor­mation. Important components of this work include speci­fying device fami­lies; specifying device-device signal carriers, levels, and timing; developing and applying stand­ard analytical, com­putational and experimental meth­ods for device modeling and char­acterization; and de­signing and build­ing devices to use in testbed applications. More->

Chassis
Leader: George Church
Our overall goals require that we build parts, devices, and systems that work inside living cells.  In an engineering sense, our cells must act as “power supplies” and “chassis,” providing materials, energy, and other basic resources that are needed for proper system function.  Here, we will develop and characterize a small number of “naïve” cellular power supplies and chassis that can be used to sustain the proper operation of any synthetic biological system over a range of defined operation conditions.  As a result, systems engineers will be able to focus on system design, and cell engineers will be able to focus on the design of cells as power supplies and chassis. More->

Human Practices
Leader: Paul Rabinow (Acting)
The defining goal of SynBERC is to make biology into an engineering discipline. To this end, Thrusts 1 through 3 link evolved systems and designed systems, with emphasis on organizing and refining elements of biology through design rules that enable the engineering of complex integrated biological systems. Thrust 4 examines synthetic biology within a frame of human practices, with reciprocal emphasis on ways that economic, political, and cultural forces may condition the development of synthetic biology and on ways that synthetic biology may significantly inform human security, health, and welfare through the new objects that it brings into the world. More ->

Bringing it together
The four thrusts will have the following common elements:

• Standardization: All parts, devices, and chassis will be defined in accordance with standards that we invent for the purpose of hiding information and making routine the details of part, device, and chassis use across a range of conditions.
• Models and Methods: For each part, device, and chassis, we will develop models that describe their function, that support design, and that direct the characterization of parts, devices, and chassis performance via experiment.   
• Composability: parts will be designed to work together as many devices, devices will be designed to combinable into many systems, and chassis will be designed to support the operation of a range of systems. 
• Evolution: Directed evolution and other laboratory-based screening and selection methods will be used to optimize the functions of parts, devices, and chassis.  Whenever evolution-based methods are used, they will be applied with the limits defined by standards and abstraction (below).
• Access & Open Biotechnology: All parts, devices, and chassis will be made available via the Registry of Standard Biological Parts. In addition, the analytical methods, design software, and data will be available as open-source to the non-profit research community and companies that are members of the industrial consortium.
• Collaboration: All four thrusts will be designed such that specific work can be progressively integrated. Designing such a model so as to contribute to human security, health, and welfare is a primary objective.