Home  Research in Cambridge iGEM programme
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Stefan Milde's powerpoint guide to the iGEM2007 competition at the University of Cambridge, and background information for iGEM2008
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Synthetic Biology Entrepreneurial Workshop
INTRODUCTION AND OBJECTIVES
Synthetic Biology is an emerging technology where engineering principles such as standardization, abstraction and decoupling and are applied to the construction of genetic parts, devices and systems. The implementation of engineering approaches to standard construction, characterization and computational modeling of these genetic building blocks will transform what is currently a bespoke industry into true genetic engineering. For the past three years we have participated in the international Genetically Engineered Machines (iGEM) competition held at MIT. Our experience shows us that “hands on” small group teaching with a high faculty-to-student ratio is a highly effective method. Moreover, the engineering-based “team structure” for project development and construction is crucial for success. Since the students come from different academic backgrounds, engineering, physical and natural sciences, our emphasis for competition is less what the students “know” and more what the students “can do” by the end of the 10 weeks. We will apply these same principles for this workshop.
The workshop will expose our undergraduate students, graduate students and post-docs to the fundamentals of Synthetic Biology, intellectual property rights and how to formulate a business plan. We will provide lectures and discussion time with experts on these topics. In the afternoon of the first day, we will divide students into 3 or 4 teams to come up ideas to exploit Synthetic Biology that will be given as 10 minute PowerPoint presentation to a panel of judges. On the second day the teams will be expected to formulate a business plan that they will give as 10 minute PowerPoint presentation to a panel of judges. The teams will be evaluated and criticised in the style of “Dragons Den”.
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WORKSHOP SCHEDULE
Synthetic Biology & Applications
Thursday 3rd of July
9:00 Registration, team selection
9:30 Introduction to Synthetic Biology, examples, enabling technologies: Drs Jim Ajioka & Gos Micklem
11:00 Coffee Break
11:30 Potential applications in Plant Systems: Dr Jim Haseloff
12:15 Risks & Ethics: Dr Jim Ajioka
1:00 Lunch
2:00 Team Project Planning
3:30 Tea Break
4:00 Team presentations
5-5:30 Discussion
Entrepreneurial training: Intellectual Property and Business Plans
Friday, 4th of July
9:00 Intellectual Property: Dr Andrew Walsh, Cambridge Enterprise
10:00 Business plans: Dr William Bains, Institute of Biotechnology
10:15 Microbial examples: Dr John Archer
11:15 Coffee Break
11:45 Entrepreneurial experience: Profs. Jim Murray & David Klenerman
1:00 Lunch
2:00 Team Planning
3:30 Tea Break
4:00 Dragons Den: Team presentations
5:30 Selection and award to the winner
SESSIONS
Each of the lectures should be limited such that 10 minutes will be left for student Q&A or discussion.
Synthetic Biology & Applications
Team selection. The participants will register (~15-20) will be divided into four teams
Introduction to Synthetic Biology, examples, enabling technologies. Drs Jim Ajioka & Gos Micklem will give an introduction to Synthetic Biology consisting of a historical perspective, the fundamental application of engineering principles to genetic systems, and technical overview. They will present published examples of research in Synthetic Biology and an overview of the enabling technologies that underpin the experiment and analysis. The session will conclude with a discussion of the risks and ethics associated with Synthetic Biology.
Applications in Microbial Systems. Dr John Archer will give an overview of the use of microbes in industrial processes and how Synthetic Biology may be applied to facilitate these processes.
Applications in Plant Systems. Dr Jim Haseloff will give an overview of the use of plants in agriculture and how Synthetic Biology may be applied to facilitate cultivation and productivity.
Risks & ethics. Dr Jim Ajioka will give a short presentation on the history and perceived risks for recombinant DNA technology and Synthetic Biology. Drs Ajioka, Haseloff and Micklem will lead a discussion on risks and ethics.
Team planning: Application of Synthetic Biology. Each of the four teams will formulate an application of Synthetic Biology to an industrial or agricultural problem using the tools described in the morning lectures. They will prepare a 10 minute PowerPoint presentation of their plan.
Dragon’s Den: Team presentation of ideas. Each team will take 10 minutes to present their plan to the panel of experts. The plans will be evaluated and criticized with a winner chosen at the end of the session.
Entrepreneurial training: Intellectual Property and Business Plans
Intellectual property. Dr Andrew Walsh will provide an overview of intellectual property, the legal implications and how it might be developed and handled in the University environment.
Business Plans. Dr William Bains will give an insider’s view of how to prepare a successful business plan and how the different types of funding may be suited to particular kinds of startup companies and intellectual property.
Entrepreneurial experience. Drs Jim Murray and David Klenerman, will present their experience in starting up a Biotechnology company.
Q & A session. The students will be able to quiz our panel of experts to help them devise their business plan based on their ideas from the previous day.
Team Planning: Development of a Business Plan. Each of the four teams will formulate a business plan guided by information presented in the morning lectures. They will prepare a 10 minute PowerPoint presentation of their plan.
Dragon’s Den: Team presentation of business plans. Each team will take 10 minutes to present their plan to the panel of experts. The plans will be evaluated and criticized with a winner chosen at the end of the session.
EVALUATION AND OUTCOMES
What the students “can do” is our primary objective in the workshop. We will evaluate their ability to: 1) apply Synthetic Biology to an industrial or agricultural problem and 2) to develop intellectual property and a business plan to exploit their ideas. The “Dragon’s Den” format for evaluation will force the students to work as a team, thinking creatively and robustly in a pressurized situation. |
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iGEM2008 Construction challenge |
Paired teams were set the challenge of constructing towers from toothpicks and marshmallows on a printed circular template - with the objective of building the highest possible self-supporting structure. The teams soon encountered the less-than-ideal properties of marshmallow as a building material. Elaborate structures gradually slumped. Yet one team discovered a novel construction technique that took them to new heights...
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Gos Micklem
http://www.gen.cam.ac.uk/Research/micklem.htm
http://www.ccbi.cam.ac.uk/
Jim Ajioka
http://www.path.cam.ac.uk/pages/ajioka/
http://www.path.cam.ac.uk/~toxo/
Jim Haseloff
http://www.plantsci.cam.ac.uk/Haseloff/Home.html
http://www.plantsci.cam.ac.uk/research/jimhaseloff.html |
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Summer competition for undergraduates and postgraduates in the biological and engineering sciences.
The University of Cambridge has sponsored entries in the intercollegiate Genetically Engineered Machine competition (iGEM2005, iGEM2006 and iGEM2007). The competition is organised from MIT, and involves teams from universities around the world (13 in 2005, 37 in 2006 and 58 in 2007). The competition takes the form of an open design challenge.
The challenge is to design and test a simple biological system from standard, interchangeable parts and to operate it in living bacterial cells.
As well as spending the summer weeks designing the system and synthesising and testing the parts, there will be the opportunity to attend an end-of-competition jamboree at MIT with the other teams. The competition ran for the first time in 2004, with the teams, from five US universities, presenting systems that performed functions from detecting caffeine to implementing bacterial photographic film. This is an opportunity for biology students to learn about approaches for organising complex systems and practical tools for design, modelling, and simulation; and for engineering students to immerse themselves in biology via their base instincts, to design and build, at the frontier of this exciting research area.
Support for the 2007 competition has been generously provided by the EU Synbiocomm Program, the Isaac Newton Trust through the UROP studentship programme, the University of Cambridge, the EPRC and DNA 2.0.
Biological components for engineering
The Biological Engineering Division of MIT's Computer Science and Artificial Intelligence Laboratory has pioneered the collection and use of modular biological components. They have established a Registry of Standard Biological Parts, which contains about 100 basic parts such as operators, protein coding regions, and transcriptional terminators. It also includes many devices such as logic gates built from these basic parts. These parts and devices, or “BioBricks”, have been developed and used by student teams to build biological systems.
Assembly of parts into devices and systems has been performed using a combination of DNA synthesis and traditional cloning techniques that allow easy construction of composite devices that, in turn, can themselves be used as parts. Simultaneous parallel assembly allows rapid construction of student projects.
Design competitions
The techniques have been used in two January classes at MIT and in the Summer 2004 Synthetic Biology Competition, a joint educational effort among students and instructors at Boston University, Caltech, Princeton, University of Texas at Austin, and MIT.
For example, in 2004 the UT Austin team chose to design and build a biofilm that could perform distributed edge detection on a light-encoded image. In theory, each cell in a lawn of bacteria would update its state in response to light input and, depending on the state of neighboring cells, decide whether or not to change color. The team used the image 'Hello World' to illuminate an approximately 10 cm square lawn of bacteria containing their initial system (the first picture encoded on their biofilm is shown). A lawn of E. coli is able to capture images at about a gigapixel per square inch.
Program
The project was held over the summer. The core group is composed of a mixture of 11 undergraduate summer students and several postgraduate/postdoctoral workers. Supervision for the group was mainly provided by Jim Ajioka (Pathology), Gos Micklem (Cambridge Computational Biology Institute), Jim Haseloff (Plant Sciences) and Jorge Goncalves (Engineering). There was an extended network of support for more specialized aspects of the work. We have had guest lectures and advice in the areas of computational biology, bacterial chemotaxis, quorum sensing, microbial imaging and fluorescent imaging.
The project was housed in the teaching laboratory at the Department of Plant Sciences. The laboratory provided a well equipped space for the experiments, with access to advanced instrumentation. The laboratory is immediately adjacent to Jim Haseloff's laboratory, and support was available in the form of reagents, glassware and advice. Direct visualisation of microbial behaviour plays a role in the project, and a suite of imaging tools was also be available for use. These include confocal microscopes, epifluorescence, low-light cameras and image analysis software.
The work program involved different phases of design, construction and testing. The design phase required (i) creating the overall concept, (ii) sketching out the genetic logic, and (iii) more detailed testing using computer modeling. Individual modules from the design were constructed and tested separately, both to speed the process by working in parallel, and to allow easier debugging of the design. Different coloured fluorescent proteins are available for rapid measurement of the states of genetic logic. The construction phase requires the synthesis of new DNA elements, and the recombination of new and existing elements in the BioBricks collection.
Web resources:
We have a University of Cambridge wiki site with more details about our entry to the competition:
And there are some details of the competition and our fellow competitors on the following sites:
MIT Registry of Parts:
iGEM2007 site |
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