Cambridge website for Synthetic Biology resources

www.synbio.org.uk

Compiled by Jim Haseloff at the University of Cambridge. SpannerPlantLogo140This 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.

Similar to the Cambridge-based Raspberry Pi and OpenLabTools initiatives, we promote the use of low cost and open source tools - in our case for use in biological engineering.

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www.synbio.org.uk

European Association of Students & Postdocs in Synthetic Biology (EUSynBioS)

EUSynBioSprelimLogo240The European Association of Students & Postdocs in Synthetic Biology (EUSynBioS) invites you to join its pre-launch community. The EUSynBioS initiative seeks to shape and foster a network of young researchers active the nascent scientific discipline of synthetic biology within the European Union by means of providing an integrative central resource for interaction and professional development.

Key objectives of EUSynBioS include i) the implementation of a central web platform for sharing news and opportunities relevant to members of the community as well as for academic networking, ii) the arrangement and support of events for academic exchange and professional development, iii) liaison with representatives of industry, and iv) establishment of a primary contact for collaboration and exchange with related communities of synthetic biology students and postdocs abroad.

Registering as a member is free and can be completed within 30 seconds via the following link http://www.eusynbios.org/students-and-postdocs/join Students and postdocs who register as a EUSynBioS member will be able to:
o Access a large network of young researchers in synthetic biology for academic collaboration and exchange
o Share technical resources and teaching materials
o Stay informed about relevant events such as conferences, workshops, or social outings o Browse relevant jobs in academia and industry
o Use site visits and mentoring opportunities to interact with prospective employers
o Connect with members of related communities all over the world

By registering as a member prior to the official launch of EUSynBioS, you will not only make a statement of support which will have an impact on the resources available to the community in the future; you will also be given the chance to actively shape EUSynBioS right from the start, and have an edge when applying for a position on the Steering Committee. We are looking forward to your joining us ! Christian Boehm, University of Cambridge.

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.

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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.

Research news at Cambridge University

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www.marchantia.org

Online resources, including bibliography, weblinks and posters, for work with the simple plant system, Marchantia polymorpha.

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OpenLabTools: open technology in Cambridge

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The OpenLabTools Project is a new initiative for the development of low cost and open access scientific tools at the University of Cambridge. With support from the Raspberry Pi Foundation, student projects include data acquisition, sensing, actuating, processing and 3D manufacturing, see the openlabtools.org website.

Research Studies

PhD Studentships in Cambridge

The Board of Graduate Studies manages admission of the University's graduate students. Prospective students should start here - for an introduction to the University of Cambridge, the courses we offer, how to apply for postgraduate study, how your application will be processed, and immigration and other important information.

Click here for more information about Cambridge