Biomaker Fayre showcases 40 open source, low-cost biological instruments

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There was a real buzz in the air on Saturday 21 October, as 40 interdisciplinary teams exhibited their prototypes for the 2017 Biomaker Challenge at the Department of Engineering.

Projects covered everything from spectrometers for measuring the colour of penguin guano, microfluidics for tissue culture, to ultrasonic systems for measuring plant height and 3D printed modular microscopes. Each group was given a £1000 grant and four months to turn their big ideas for open source and DIY research tools into reality and over 100 people came along to the final event.

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The Challenge and Fayre aimed to show the value of open, low-cost and DIY technologies as convening points for interactions between biologists and engineers. They are also important educational tools for those who are interested in developing technical skills and have great potential for improving the quality of science and increasing productivity in the lab for lower costs. With the proliferation of digital designs for 3D-printing and easily available consumer electronics like Arduino which has a huge community of users and lots of online help, designing your instrumentation around your experiment rather than vice versa has never been more possible.

Winners of the 3D-printed awards were:

Best Technology: A low-cost chromatography system for protein purification

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Stéphanie Polderdijk (Cambridge Institute for Medical Research) and Wolfgang Schmied (MRC LMB) set out to lower the cost of column chromatography: a routine technique for the separation of components from complex mixtures.

In biochemistry and molecular biology, proteins frequently need to be purified by gravity flow, centrifugation, which are time-consuming or by using expensive automated systems that use pumps to force solutions over a column. They produced a lower cost, modular, open-source alternative to these commercial systems for performing simple, routine purifications.

Best Biology: PiRMA: A low-cost rodent physiology monitoring bed for pre-clinical experiments

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Marcel Gehrung, Dominick McIntyre and Lina Hacker (all from CRUK Cambridge Institute) developed a low-cost rodent physiology monitor which is suitable for a wide range of experiments and imaging applications such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Parameters such as Heart Rate (HR), Respiratory Rate (RR), and Temperature can be measured which are important to reduce data artefacts. Existing solutions are in the cost range of several thousand pounds and do not support the holistic workflow required in animal experiments.

Maker Spirit: A DIY focus stacking system for macrophotography of developing ferns 

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Jennifer Deegan (Department of Plant Sciences) and team Matthew Couchman (John Innes Centre), Tim Deegan (CohoData) and Richard Mortier (Computer Lab) developed a  very low-budget  focus stacking system for microphotography in order to take a series of photographs showing the development of the fern gametophyte from the very earliest feasible stage to the appearance of the first sporophyte leaf. 

Dr Jenny Molloy, co-organiser of the Biomaker Challenge and Fayre reported that “the judging panel were hugely impressed by the progress the teams made over just four months and we're excited to see where people go next with these open source designs, that are free for anyone to download, replicate and build on in their own labs”.

See more photos from the day here >>

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Biomaker Challenge 2017 was jointly funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1 and the Isaac Newton Trust.

The Biomaker Challenge and Biomaker Fayre were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative and the CambridgeSens Network.

Thank you also to our sponsors ARM Ltd and New England Biolabs.

New OpenPlant Fund call for training materials

The aim of the fund is to promote the development of plant synthetic biology and cell-free systems as interdisciplinary fields and to facilitate exchange between the University of Cambridge, the John Innes Centre, and the Earlham Institute for the development of open technologies and responsible innovation in the context of Synthetic Biology.

A wealth of tools, technologies and methodologies for plant Synthetic Biology have been developed through OpenPlant, the OpenPlant Fund, the Biomaker Challenge, and complementary efforts. In this call, we encourage applications for projects that will provide training or knowledge exchange to broaden the use of plant synthetic biology and cell-free tools.

Eligibility

Applicants and teams:

  • Primary applicants should be students or staff at the University of Cambridge, John Innes Centre or the Earlham Institute. External team members are welcome.
  • Interdisciplinarity within the team is a judging priority but teams from the same background are not excluded.
  • Where possible, projects should build collaborations between the University of Cambridge and a Norwich-based OpenPlant partner institute: the John Innes Centre or the Earlham Institute.

Proposals:

  • All proposals must lead to tangible, publicly documented and open outcomes which demonstrate interdisciplinary thinking.
  • Applications for travel or event funding without justification of how this will lead to a tangible outcome or resource will not be considered. Salary or stipend costs will not be funded.

Contact Details

Please contact Dr Colette Matthewman with any enquiries at colette.matthewman@jic.ac.uk or on +44 (0)1603 450267.

More information at: https://www.openplant.org/fund/

More information at: https://www.openplant.org/fund/

Hackster.io platform for Biomaker projects

We have set up a new platform for Biomaker projects on hackster.ioHackster.io is a very interesting new platform that supports the documentation of open source projects, and community building. It boasts over 280,000 members, and support from all major hardware manufacturers, retailers and open-source communities. It allows simple documentation of hardware projects, and provides a way of linking between projects that share components or authors. So it is a great way of building a linked community - with the benefits of global access and interconnectivity.

www.hackster.io/biomaker/

www.hackster.io/biomaker/

Individuals can start to build a portfolio of projects - and gain wider recognition for their efforts, with a link that can be used for one's CV or embedded in a personal website.

We have long term plans for Biomaker - and will definitely run the event in coming years - where we are keen to encourage follow-up and expansion into more overtly biological areas. For example, we are considering offering cell-free systems as part of next year’s challenge. The hackster.io platform should be helpful for this. We're hoping that the hackster platform will help build links between our academic lives and open-tech communities - giving us the opportunity to both build technical portfolios (that are CV-quotable), and open the work to a wider audience.

The hackster.io platform supports Github - so you can include all existing GitHub documentation. The hackster project layout is better suited to project description that GitHub - so may be an easier choice in the longer term - where GitHub can be still be used used for software documentation (which is what it excels at).

Contact Jim Haseloff or Jenny Molloy for further details.

Open Technology Week in Cambridge

Open Technology Week: a celebration of all things tech and free to share - includes an open event  on Saturday 21st October 2017, the Open Technology Workshop and Biomarker Fayre at the Engineering Department, Trumpington Street, Cambridge. The event will include a programme of provocative and intriguing talks in the morning, followed by demonstrations and prize-giving for this year's Biomarker Challenge projects - great inspiration for anyone who anyone who would like to join in next year, or is just plain curious! Details will be posted at synbio.cam.ac.uk

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Biomaker Challenge August Meetup: Arduino shields and touchscreen displays

Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. From colorimeters to microfluidics and beyond, we’re looking for frugal, open source and DIY approaches to biological experiments. A list of funded projects can be found here

Thie second Biomaker Challenge meetup took place on Wed 30 August and was a great opportunity for those who came along to meet other participants, share ideas and get help with various aspects of the challenge. 

The teams got an introduction to using the Gtronics Proto Shield Plus with Arduino and programming the 4D Systems Display Programmable Touchscreen

Biomaker Challenge - building collaborations through low-cost instrumentation

Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. The programme aims to facilitate exchange between the biological and physical sciences, engineering, and humanities for the development of open source biological instrumentation using commodity electronics and DIY approaches.

The inaugural 2017 cohort comprises 130 participants working in 41 teams on biological and biomedical devices, instruments, and sensors.  Participating teams received a Biomaker Toolkit and a discretionary budget for additional sensors, components, consumables, and mechanical fabrication worth up to £1000.

Teams of all sizes were considered for the grant and range from an individual to twelve people. Interdisciplinarity within participating teams is prioritised and although most participants are students or staff at the University of Cambridge, John Innes Centre or the Earlham Institute, external team members are welcome and included designers from the Royal College of Art, computer scientists from ARM, local artists, makers, and entrepreneurs.

During the challenge, we offer assistance and support providing components and access to prototyping facilities in Cambridge such as Cambridge Makespace and the Media Studio on the Cambridge Biomedical Campus. We also run periodic technical workshops and meetups to encourage teams to interact and help share skills and ideas. Participating teams will document a full set of assembly/fabrication instructions, images, and a list of components used, which are made publicly accessible via GitHub. This will enable others to replicate and build on their work for their own research questions. The challenge culminates on 21 October 2017 in a public exhibit, the Biomaker Fayre, where participants will demonstrate their creations and prizes will be awarded for especially creative and enabling projects.

The Challenge will repeat in 2018 and we look forward to seeing the projects develop with a new cohort of participants to further increase access to low-cost, open access biological tools and technologies.


EXAMPLE PROJECTS

Real-Time monitoring of cell proliferation

An absorbance sensor that can be used inside a cell culture incubator for real-time monitoring of culture medium pH and cell density. The system is able to automatically transmit this data to an email server for remote monitoring of cultured cells.

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Microfluidic Turntable for molecular diagnostic testing

An Arduino controlled turntable with a stroboscope for disk visualisation on screen and optical detection for absorbance and fluorescence measurements. The disc, fabricated using a laser cutter and paper plotter, is rotated by an Arduino controlled motor. Fluid actuation is also controlled by Arduino, changing the rotation direction and revolutions per second to achieve pumping, mixing and separation.

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A programmable staging mount, and an imaging platform for a microfluidics based conditioned learning hub for motile bacterial cells.

By developing a maze traversal challenge, different scenarios for chemotactic bacterial colonies to employ their decision-making machinery and navigate through the maze will be assessed. This may lead to an understanding of cognition, memory and learning in bacterial colonies.

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