SpannerPlantLogo140Cambridge website for Synthetic Biology resources
 
 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. 
 
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.
 

SynBio calendar

  • 29 May

    With their provenance as an excellent source of pharmaceutical, neutraceutical and health promoting chemistries, plant natural products are an attractive target for biotechnological development for industrialization

  • 08 Jun
    07:00 PM to 07:00 PM

    (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 pin-point the challenges,

  • 09 Jun
    07:00 PM to 07:00 PM

    Algae Innovation Center (AIC) Lolland commenced in 2010 as a project between Green Center, Roskilde University and Aalborg University with the aim of identifying and researching the potentials of using

  • 15 Jun
    07:00 PM to 07:00 PM

    The conference will focus on frontiers in biological design, synthetic biology and processing, bringing together the top academic, industrial and governmental researchers from both the East and the West. Specific

  • 22 Jun
    07:00 PM to 07:00 PM

    A hands-on Summer Course of advanced Genetic Engineering of Bacteria at the onset of the SynBio era.

  • 24 Jun
    07:00 PM to 07:00 PM

    GCAT-alog is freezer management software, optimized for use by synthetic biologists. GCAT-alog is freely available to use though no support other than the user manual is available.The tools can be accessed

  • 28 Jun
    07:00 PM to 07:00 PM

    This week-long summer school provides advanced training in history of the life sciences, a lively international field that offers a long-term perspective on some of the most significant ideas, practices

  • 08 Jul
    07:00 PM to 07:00 PM

    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, UK. This meeting

  • 09 Jul

    SynBioBeta is a forum to bring together synthetic biology startups as well as other stakeholders in the ecosystem. This evening event will be held during the BioBricks Foundation SB6.0 Conference. The

  • 11 Jul

    2nd International Synthetic Yeast Genome Consortium Meeting held in the UK at Imperial College London - bringing those around the world involved in the Sc2.0 project together to discuss progress and opportunities.

29 May - 14 Jun
09 Jun - 20 Jun
22 Jun - 28 Jun
28 Jun - 11 Jul
09 Jul - 12 Jul

SynBio Google newsfeed

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£17k Nerve KickStart challenge

CamElBannersmallInnovative global startups are being invited to tilt at a £17k prize package in the Nerve KickStart competition, run in conjunction with the Nerve conference on disruptive technology in Cambridge from June 25-27. KickStart is strictly for 'killers' - entrepreneurs whose fledgling ventures deal only in game-changing technology. Entries are invited now from around the world and 12 shortlisted candidates will be invited to pitch to international entrepreneurs throughout the Nerve conference before a final-day showdown for the £17k prize pot.

The sponsors are all global innovation influencers - led by superchip designer ARM and technology design hothouse TTP in association with Trademark and patent attorney Mathys & Squire; Cambridge co-working community ideaSpace; and Business Weekly's social network for startups, Cambridge Elevator. The winner-takes-all competition provides £5k in cash, an Intellectual Property advisory package worth £5k, and a membership arrangement at ideaSpace valued at £7k.

Cut-off date for entry is June 14. The 12 shortlisted entrants will be notified by June 17 and invited to pitch live on stage at Nerve - www.itsnerve.com - to delegates and the KickStart panel. Startups can only enter online through the entry page at www.cambridgeelevator.com

Call for exhibits and experiments at GROW YOUR OWN...

ScienceGallery logoGROW YOUR OWN... is a curated, open call exhibition tackling provocative questions raised by synthetic biology to be hosted at the Science Gallery, Dublin (http://sciencegallery.com), supported by the Wellcome Trust. The exhibition is curated by Professor Paul Freemont (Imperial College), Professor Anthony Dunne (Royal College of Art), Cathal Garvey, Daisy Ginsberg (www.daisyginsberg.com) , and Professor Michael John Gorman (Science Gallery), GROW YOUR OWN... offers audiences a participative experience to explore the possibilities and potential implications of synthetic biology, through an exhibition, events and workshops.

The organisers are interested in works that offer a participative and interactive visitor experience for a broad age range of visitors, especially those aged 15-25. We seek projects that inform, intrigue, provoke dialogue and engage audiences about an unfamiliar, complex and far-reaching topic, moving forward a public conversation about synthetic biology. Funding up to £5000 is available. More details are available at: http://sciencegallery.com/growyourown - The call closes at 12 midnight on May 26th 2013.

Senior Internships for Interdisciplinary Research

CambUni 52Applications are invited for the next round of University of Cambridge / Wellcome Trust Senior Internships. The scheme is aimed at suitably qualified post-doctoral candidates with backgrounds in the physical sciences (incl. engineering, mathematics and computer sciences) who wish to gain experience in the application of their research to solve problems in the basic biological and biomedical sciences. Projects in Synthetic Biology are available in the Haseloff laboratory.

Research projects must fall within the broad remit of the Wellcome Trust and the research must be undertaken in laboratories within the School of Biological Sciences or the School of Clinical Medicine. In exceptional circumstances candidates with a background in the life sciences wishing to gain experience working in the physical sciences may also be considered, but additional restrictions apply. 

The internships are intended to provide opportunities for award holders to gain experience in applying biological approaches, and/or apply novel theoretical or experimental techniques from the physical sciences to address biological problems. In addition, it is hoped that this scheme will foster longer-term collaborations between Principal Investigators from the physical and life sciences disciplines within the University of Cambridge.

Senior Internships will be awarded for periods of 3-12 months.  Further details on the scheme and the application process can be found at http://www.admin.cam.ac.uk/offices/rso/internal/issf/ Funding is available for up to 12 months, Salary: £27,854 - £36,298. Quote Reference: AK28312. Closing Date: 29 May 2013

Raspberry Pi Summer Internship Programme (2013)

RaspiModelB200We are looking for approximately ten students to take part in a range of projects that make use of the Raspberry Pi computer. A list of projects can be found below. Alternatively, if you have an interesting project idea of your own, please contact the programme organiser (Robert Mullins). The tutorials created by last year's summer students can be found here. A few more details:

You must be a Cambridge Undergraduate NOT in your final year of study. Applications from students in all departments are very welcome. The placements last 10 weeks from the 24th June to 30th August. You will recieve a bursary of 400GBP/week to cover your accommodation and other expenses. To clarify, this placement is not classified as employment, rather it is a training opportunity to help you develop technical and transferable skills. If you are interested in one of the projects below, please email the contact named. Alternatively, if you would like to propose a project, please email Robert Mullins. While you will be based in your supervisor's department, we are planning a number of events to ensure that all of the summer interns are brought together during the programme. A condition of taking part in the programme is that you agree to release any intellectual property that you develop whilst working on the programme into the public domain, i.e. you will be expected to write up you project and release text and code (under an appropriate FSF approved license). If you have any questions please do not hesitate to contact Robert Mullins.

Project Team 1: "Sensing and data logging with a Raspberry Pi"

Supervised by: Jim Haseloff ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ), Simone Hochgreb ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ), Alexandre Kabla ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). Places available: 2-3. Requirements: Skills in programming and/or electronics.

Sensing and monitoring of environmental parameters is ubiquitous in engineering. Typical systems in industry andlabs include a sensor, a data conditioning module, and a personal computer or data logger to connect the signals to a readable output. Today, most smart phones have sufficient processing and memory capabilities to allow data acquisition for most common laboratory experiments. Yet we continue to use dedicated PCs and data acquisition boards at a high cost. We would like to offer projects aiming to create simple, low cost solutions to data acquisition and logging for most generic educational and laboratory purposes. Students will work as a team and explore various technical approaches (using off-the-shelf solutions, interfacing with Arduino boards, or developing custom circuits) with delivery to local/remote dataloggers via different protocols. The production of detailed tutorials will represent an important part of the work. Potential student projects within this theme:

Novel sensors and data acquisition with the RPi

High speed data transfer through SPI

Networked data logging

During this project the student will: learn about sensing and data logging technologies, develop her/his team working skills, and improve her/his communication skills by presenting results and generating public domain documentation

Project Team 2: "Versatile imaging platform using a Raspberry Pi"

Supervised by: Jim Haseloff ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ), Simone Hochgreb ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ), Alexandre Kabla ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). Places available: 2-3. Requirements: Skills in programming and/or optics.

A large number of tasks in materials characterisation, biological analysis or medical diagnostics rely on the detection of specific features in images. Most applications do not require particularly high frame rates or resolutions and a webcam often provides sufficient image quality. Current professional software and off the shelf systems are costly. This creates an opportunity for developing inexpensive hardware and software solutions that may do the job just as well. The Raspberry Pi and its new camera module offer fantastic opportunities to develop an open platform for imaging. Two students will work in concert to develop control software, optical components, and produce tutorials. Potential student projects within this theme:

Image acquisition with the RPi - Software project using the new camera module of the Pi

RPi based table-top chassis for automated optical measurements.

RPi controller for environmental sensing and control of biological samples

During this project the student will: learn about imaging, image processing and microscopy, develop her/his team working skills, and improve her/his communication skills by presenting results and generating public domain documentation

Additional projects: "Building a lightweight RFID tag reader platform using Raspberry Pi by integrating OpenBeacon RFID USB reader", and "Adventures with Raspberry Pi"

(see http://www.cl.cam.ac.uk/projects/raspberrypi/summer/)

Autodesk Cyborg

25bits-cyborg-tmagArticle-v2

 

Autodesk, pioneer of personal computer-aided design software, announced its foray into the emerging nanoscale world of synthetic biology and materials. For the last two years, a small group of software engineers and molecular biologists have been developing a software system for designing at the molecular level at the company’s research laboratory in downtown San Francisco. Autodesk have introduced “Project Cyborg,” a Web-based software platform for delivering a range of services like molecular modeling and simulation.

“People are only now being introduced to the fact that this form of science is in fact design, and it has the same paradigms and patterns as designing a factory or designing a car, with different nouns and verbs,” said Jeff Kowalski, Autodesk’s chief technology officer. “That’s our objective – to understand how to take 30 years of technology to transform how design is done in the inert world and empower those who are designing in the living world.

Thomas Knight, an M.I.T electrical engineer, introduced the concept of biobricks in 2003. The idea has been to create a library of standard biological parts derived from specific DNA sequences. Ideally they would share a common “interface,” making it possible to use them to construct new biological systems. A striking example of the potential of molecular design was announced in February 2012 by the Wyss Institute for Biologically Inspired Engineering at Harvard. Two scientists at the institute designed a robotic device from DNA that was intended to seek out specific cells and deliver anticancer therapeutics with remarkable precision. The nanoscale robot is shaped like a clamshell and designed to open when it reaches its target, releasing a specific molecule.

The Autodesk researchers acknowledge they are far from being able to sell commercially robust engineering tools for the nano world. “Right now we don’t even have the notion of digital prototyping in any mature way in biology,” said Carlos Olguin, head of the Autodesk Bio/Nano/Programmable Matter Group. “People really do all of this by trial and error.” But the company is placing a significant bet that that will not always be the case. If Autodesk is right, it will be a tremendous vindication for K. Eric Drexler, an M.I.T.-trained engineer who in the 1970s began forecasting the emergence of a world engineered by nanoscale machines.

See NY Times article: http://bits.blogs.nytimes.com/2013/02/25/for-autodesk-a-step-into-a-nanoscale-world/

Autodesk: http://www.autodeskresearch.com/projects/cyborg

Top British Innovations

Britinnovatnhttp://www.topbritishinnovations.org 

See a list of great British innovations - To celebrate the theme of invention and discovery in National Science & Engineering Week the sponsors want the public to vote for the most important innovation in science and technology from the last 100 years and the one likely to shape the future.

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