Cambridge website for Synthetic Biology Resources
 
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Compiled by Jim Haseloff at the University of Cambridge
This site contains details of recent papers and activity in Synthetic Biology, with particular emphasis on: (i) development of standards in biology and DNA parts, (ii) microbial and (iii) plant systems, (iv) research and teaching in the field at the University of Cambridge, (v) hardware for scientific computing and instrumentation, (vi) tools for scientific productivity and collected miscellany. 

 

www.synbio.org.uk

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SynBio calendar

  • 18 Feb

    Technology is driving revolutionary changes in biology. Over the past decade, scientists and engineers have begun to define the path forward in the genomic era. Systems Biology has arisen...

  • 17 Mar

    Now that we know the sequences of many genomes, from a wide variety of organisms and even from individuals with unique characteristics, many researchers have turned to making intentional...

  • 09 Apr

    The developments within synthetic biology promise to change the world in significant ways. Yet synthetic biology is largely unrecognized within conservation. The purpose of the meeting...

  • 09 Jun

    (Re-)constructing and Re-programming Life This conference will provide an in-depth discussion forum among practitioners of the various fields underlying Synthetic Biology. It aims to...

  • 09 Jul

    The BioBricks Foundation is pleased to announce The BioBricks Foundation Synthetic Biology 6.0 Conference (SB6.0), which will take place on July 9-11, 2013 at Imperial College, London,...

  • 30 Jul

    This course will focus on how the complexity of biological systems, combined with traditional engineering approaches, results in the emergence of new design principles for synthetic...

18 Feb - 23 Mar
09 Apr - 15 Jun
09 Jul - 13 Aug

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Synbio news:
11 Jun 2011

Bio coder: Christopher Voigt, an assistant professor at the University of California, San Francisco, is developing software to speed up designing microbes that produce biofuels and other useful chemicals. 
Credit: Technology Review

COMPUTING

Software for Programming Microbes

A simpler way to modify microbes could help produce biofuels and drugs efficiently.

  • From: Technology Review WEDNESDAY, JANUARY 5, 2011
  • BY KATHERINE BOURZAC

Genetically modified microbes could perform many useful jobs, from making biofuels and drugs, to cleaning up toxic waste. But designing the complex biochemical pathways inside such microbes is a time-consuming process of trial and error.

Christopher Voigt, an associate professor at the University of California, San Francisco, hopes to change that with software that automates the creation of "genetic circuits" in microbes. These circuits are the pathways of genes, proteins, and other biomolecules that the cells use to perform a particular task, such as breaking down sugar and turning it into fuel. Voigt and colleagues have so far made basic circuit components in E. coli. They are working with the large California biotechnology company Life Technologies to develop software that would let bioengineers design complete genetic circuits more easily.

Designing a microbe for a particular task would then be much like writing a new computer program, says Voigt. Just as programmers do not have to think about how electrons move through the gates in an integrated circuit, he says, biological engineers may eventually be able to design circuits for genes, proteins, and other biomolecules at a level of abstraction. "If we apply computational processes to things that bacteria can already do, we can get complete control over making spider silk, or drugs, or other chemicals," he says.

Certain types of circuits could, for instance, help regulate the activity of bacteria that produce biofuels. Instead of outside controls, internal circuits could maintain the chemical levels and other conditions needed to keep bacteria producing at high yields. "We're trying to make the cell understand where it is and what it should be doing based on its understanding of the world," says Voigt. Trying to design such a control circuit without the help of a computer would take a lot of trial and error.

Voigt has now made a type of circuit component called a NOR gate in E. colibacteria. NOR gates can be combined to perform any logical operation. In work described in the journal Nature, Voigt's group also showed they could improve the quality of the output of bacterial circuits by having them work collectively, forming a circuit of NOR gates, one in each cell. Voigt has designed bacterial circuits to hook into natural bacterial communication systems called quorum sensing, so that the cells can "vote" on an output. This increases the quality of the computation peformed.

"This breakthrough work in synthetic biology expands our capacity to construct functional, programmable bacteria," says James Collins, professor of biomedical engineering at Boston University who is not affiliated with Voigt's team. Collins observes that the California researchers have learned to combine simple circuits in individual cells to make a more complex circuit at the population level. "This represents an important step towards harnessing the power of synthetic ecosystems for biotech applications," he says.

VIDEO

The University of California researchers are now entering the second year of a research agreement with Life Technologies to develop software to automate the biological design process. "The vision is to take these software modules and develop them so that the process of biological parts selection and circuit design is far more automated and simplified than it is today," says Todd Peterson, vice president of synthetic biology research and development at the company. The company hopes to incorporate most of the software modules being designed by Voigt's group into its Vector NTI software by the end of spring 2012.

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