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Cambridge-Norwich Biomaker Challenge 2019

The BBSRC-EPSRC OpenPlant Synthetic Biology Research Centre sponsors the Biomaker Challenge for students or staff working at the University of Cambridge and the John Innes Centre and Earlham Institute, Norwich. Teams based in these institutes can include additional participants from anywhere on the planet. The Biomaker Challenge provides opportunities to work with an interdisciplinary team to identify and solve lab or field challenges, learn to use code-free programming for hardware and user interface development, develop biological applications, scientific instruments and real-world tools, or develop new ideas.

Biomaker Challenge is a five-month programme challenging interdisciplinary teams to (i) build low-cost sensors and instruments for biology or (ii) develop some biological resource or outreach project (non-hardware track).
Hardware Track: In the hardware track, we’re looking for frugal, open source and DIY approaches to biological experiments - from colorimeters to microfluidics and beyond. Whether you’re a biologist looking to optimise your protocols and pick up some electronics knowledge, an engineer looking to apply your skills and gain experience of practical biology, a designer, artist, maker, or you’re just curious and interested to participate, we’re keen to hear from you!
Non-Hardware Track: Alternatively, we are keen to support original ideas that don’t involve hardware development - such as development of a new synthetic biology tool or resource, or social science, capacity-building, design or outreach activity. We will fund individuals or groups, but want projects to support interdisciplinary activities and sharing. To this end, we will be running regular mixer and training events during the summer, and have established a global platform for documentation and exchange of Biomaker project information.

Timeline for the 2019 OpenPlant Biomaker Challenge

Biomaker is sponsoring a number of technical challenges in 2019 - these provide an opportunity for non-experts learn how to use XOD graphical programming resources to build new hardware instruments with touchscreen displays. The OpenPlant Biomaker Challenge is open to members and affiliates of the University of Cambridge and the John Innes Centre and Earlham Institute, Norwich (Click here for details). In addition, we are supporting a number of pump-priming activities to promote international participation in the Biomaker Challenge (More details here).

The BBSRC-EPSRC OpenPlant initiative (https://www.openplant.org) is supporting the Biomaker Challenge for biologists, engineers and programmers to design and build software modules and hardware devices in Cambridge and Norwich. We use the graphical Arduino programming environment, XOD (https://xod.io) to simplify the integration of low-cost sensors, displays and actuators for biological applications. No programming experience required. We provide a starter kit and links to software resources. Participants each receive an Arduino Starter Kit with 30 accessory components, and share a team kit including a 4D Systems programmable touchscreen, Totemmaker chassis hardware plus funds worth up to £1000. There will be a chance to demonstrate progress with the projects in late July, and to pitch for an additional £2000 of follow-on funding. The projects must be documented and publicly accessible. We're using the hackster.io platform for development of project portfolios and connection with that very large community (~970,000) of open source hardware hackers and technical experts. (see https://www.hackster.io/biomaker for examples of Biomaker projects).

Current 2019 OpenPlant Biomaker projects include:

  • An open-source dynamic light scattering device for nanoparticles sizing

  • LunaFlow: Bioluminescent plankton for 3D flow visualisations of pressure fields

  • Pressure controlled micro-manipulation of bioluminescent microorganisms

  • Stress priming for improved production of biotech-relevant compound in green alga

  • Mechanisms for direct electron transfer (DIET) between Geobacter and Methanothrix

  • Diabetes diagnosis and management using Arduino and mobile user interface

  • Developing an Open & Affordable 3D Bioprinter

  • Droplet-based microfluidics to mimic the compartmentation of metabolism in multicellular systems

  • e-CO-SENSE – Biophotovoltaic Powered Soil Sensors

  • An open toolkit for engineering microbial interactions

  • Establishing a joint UK-Kenya Phytoplasma research initiative

  • Build Your Own DNA Dave

  • Low Cost SLM Interface Board for Advanced Microscopy

  • SAFE - Safe Air For Everyone

  • Variable-time cameras with image recognition for inexpensive, large-scale monitoring of plant pollination events

  • Low Cost Oxygen Sensor for Bioreactors

  • MACRO IMAGER: a low-cost multi-purpose large area macro digital photography phenotyping station

  • A behavioural chamber to evaluate rodent forelimb grasping performance

  • Low cost Incubator to grow mycelium biotextile

  • Aeroponics for All

  • A neural sensor for early-stage cancer detection

  • In-situ 3D visualization using X-ray CT during mechanical testing of natural cellular materials

  • BrewerMicro – DIY microscope for counting yeast

  • IoHeat

  • Did the organellar transit peptide duplicate itself to make a disordered linker protein?

  • Identification of genes involved in chloroplast division by comparison of temporal transcriptomics of C. reinhardtii and A. thaliana

  • Engineering Low-cost Turbidostat Systems for Running Microbial Evolution Experiments

In addition, we are helping to build projects in Egypt, Ghana, Ethiopia, South Africa and Australia. More information about the Biomaker Starter Kit: https://www.biomaker.org/2019-starter-kit, and hardware and tutorial resources at: https://www.biomaker.org/tutorials.

Basic Biomaker building and team activities that are underway:

  1. Call Opens: Monday 8 April 2019
    Eligibility and details of the application process can be founds at the following page: Apply now. Application requires submission of a short form containing a description of the team, intended project and any necessary materials. Individual or team applicants should indicate whether they wish to enter the Hardware or Non-Hardware Tracks (those on the latter track won’t receive a Starter Kit).
    Mixer in Cambridge: week of 22 April 2019 (Norwich - Cambridge transport can be arranged if you let us know beforehand)
    An introductory and mixer event will be held during the call period. This will provide opportunities for team-building, discussions about potential projects and introduction to technical resources and expertise that are available.

  2. Call closes: Monday 13 May 2019
    Completed application forms will need to be submitted by this date. Proposals will be evaluated by an interdisciplinary panel of experienced biologists, programmers and engineers. Proposals will be judged on technical novelty, feasibility and likely benefit for promoting inter-institutional links and interdisciplinary working. Successful proposals will be awarded funds of £750, and those in the Hardware Track will receive a Biomaker Starter Kit worth around £250. Funds will be transferred to accounts held by the local institutional sponsors. (There is an opportunity to receive additional funding of up to £2000 following a successful progress report and pitch for further support in July - see item 5, below)

  3. Challenge Begins: Friday 24 May 2019
    The teams will be provided with a low-cost development platform based on the Open-Smart Rich UNO R3 board, which contains a variety of embedded components. The board is Arduino compatible, and can be programmed directly from the graphical programming environment XOD. We also provide a 4D Systems programmable touchscreen display for building sophisticated user interfaces.Teams will also have access to their supplementary funds, to purchase additional components for their project. There are a number of mixer and training events scheduled over the months of June and July to promote interactions between the teams and sharing of new hardware and software resources. As the projects progress, we expect the teams to document their progress on the Hackster Biomaker platform. This is an easy-to-use, open and accessible vehicle for project descriptions, that has a large worldwide audience.

  4. Progress report: Monday 29 July (OpenPlant Forum)
    Teams will get together and present progress with their projects at a meeting in late July. This event will form part of the OpenPlant Forum, and annual forum that will be held in Cambridge this year. Teams will be expected to present a short summary of their project, and will be considered for the award of additional follow-on funding (up to £2000), based on their progress described on the Hackster Biomaker site, presentation and proposed use for the additional funds. Again, a panel of experts will be convened for the judging, and additional funding will be transferred to successful teams.

  5. Advanced project building
    Teams can continue their project work through August, September and October.

  6. Challenge Closes/Open Technology Workshop: Wednesday 6th November (note change of date from 2nd Nov)
    The Biomaker Challenge will finish with a public exhibition for all teams at the annual Open Technology event in Cambridge. Awards for Best Biology, Best Technology and Best Biomaker Spirit will be awarded on the day.


Judges


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SARA-JANE DUNN

Scientist with Biological Computation group at Microsoft Research Cambridge, Affiliate PI at Wellcome-MRC Stem Cell Institute at University of Cambridge

Sara completed her undergraduate and postgraduate training at the University of Oxford, first obtaining a Masters in Mathematics, followed by a DPhil in Computational Biology from the Department of Computer Science.

Her research sits at the interface of mathematics, computer science and biology; more specifically focusing on the concept of biology as computation, in which the biochemistry of the cell performs information processing in the service of decision-making. Towards this, she collaborates with experimentalists at the Universities of Cambridge and Padova to investigate stem cell decision-making throughout Development. As a computational scientist in biology, her goal is to identify the necessary abstractions to develop predictive, explanatory models of the biological programs that govern cellular behaviour. Ultimately, this research will lead us to make cells programmable, which could fundamentally transform medicine, agriculture and even the ways we generate energy.


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EMRE OZER

Principal Research Engineer, Arm Research

Emre joined Arm in 2005. He received his PhD in North Carolina State University (NCSU) in 2001. His research topics are energy-efficient architectures, flexible electronics/ICs, fault tolerance, machine learning algorithms/hardware and biocomputing. He has published over 50 peer-reviewed papers, and holds over 20 US patents. He has represented Arm in many European projects since 2008 including Hipeac1-5, EuroCloud, and TCLS ARM for Space. Currently, he is the technical coordinator of the Innovate UK project called “PlasticArmPit” developing bespoke ML compute engines on plastic that are tightly coupled to plastic e-nose sensors.


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NEIL HALL

Director, Earlham Institute

Neil has been working in genomics for over 15 years. He has previously led research groups at the Sanger Institute, The Institute for Genomic Research, and The University of Liverpool. His research focusses on comparative and evolutionary genomics in pathogens (particularly parasitic protists) to understand the molecular basis of important phenotypes such as virulence and host specificity. His group also apply genomics to the analysis of microbial communities in order to understand how they may influence health or respond to changing environments. Neil serves on the Wellcome Trust Biomedical Resources Committee and the BBSRC Exploring New Ways of Working Strategy Panel. 


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JENNIFER GABRYS

Professor, Chair in Media, Culture and Environment, Department of Sociology, University of Cambridge

Jennifer joined the University of Cambridge in October 2018. Previously, she was Professor in the Department of Sociology at Goldsmiths, University of London, where she continues to have an affiliation as honorary Visiting Professor. She has also been a visiting Research Fellow at the Digital Cultures Research Lab in the Centre for Digital Cultures, Leuphana University of Lüneburg, Germany.

Since 2013, she has been the Principal Investigator on the ERC-funded project ‘Citizen Sense’ -- a pioneering investigation into the public engagement with environmental sensing technologies and citizen-data generation in both urban and rural locations in the US and the UK. Gabrys has been awarded an ERC Proof of Concept grant, ‘AirKit’ (2018-2019), to further develop Citizen Sense research. The Citizen Sense project has received multiple awards, including the John Ziman award for public engagement in science and technology awarded by the European Association for the Study of Science and Technology (EASST) in 2018.

Gabrys received her PhD from McGill University, and her MLA and BA from the University of Minnesota.


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RICHARD HAMMOND

Technology Director and Head of Synthetic Biology, Cambridge Consultants

Richard is an experienced R+D leader working at the interface between engineering and life-sciences. His works aims to take research ideas and discoveries and translate them into widely-available products to improve people's quality of life. Richard is responsible for building Cambridge Consultants' business and technical capabilities in DNA-based technologies, particularly around the growing discipline of synthetic biology.


Contact Details

Please contact biomaker@hermes.cam.ac.uk with initial enquiries.
OpenPlant (Cambridge) and the University of Cambridge Synthetic Biology Strategic Research Initiative: Alexandra Ting (synbio@hermes.cam.ac.uk)
OpenPlant (Norwich): Dr. Dieuwertje van der Does (Dieuwertje.Van-Der-Does@jic.ac.uk)

The Biomaker Challenge is funded by BBSRC/EPSRC through OpenPlant Synthetic Biology Research Centre (www.openplant.org) and supported by University of Cambridge Research Policy Committee through the Synthetic Biology Strategic Research Initiative (www.synbio.cam.ac.uk).


Support

Thanks to Totemmaker for their technical support and subsidy for Biomaker chassis materials. These allow us to introduce flexible chassis design and assembly into Biomaker. Totemmaker have created highly adaptable mechanical systems for assembling DIY chassis, lab devices and robots, using modular plastic beams and metal brackets. These have been used to build a wide variety of subsystems and assemblies, and fit well with the Biomaker approach.

More details of the systems and products can be found at: https://totemmaker.net

Looking to get involved?

Have a burning idea for a project? Looking for partners to help out? Post on our new Team Building forum and we'll help match people and projects - or you can nominate an individual project, cast for partners, ask for advice or volunteer to help.

See more details about the different schemes for international participation in Biomaker, and find details of the Cambridge-Norwich application process under the “Funding” menu item. For more information, contact Alexandra Ting (synbio@hermes.cam.ac.uk).


Opportunities for collaboration in 2020

Since 2014, we have funded small interdisciplinary projects and catalysed new collaborations between several hundred students, researchers and academics across Cambridge, Norwich and beyond. A comprehensive listing of these projects is provided here, along with links to open resources generated during the work. The projects have generated a large number of electronic prototypes, software, 3D printed devices and biological elements. We hope that these resources prove useful and can be built upon by others, especially as initiators for new low-cost approaches to quantitative biology and engineering for teaching and research. Please contact us if we can assist in any way.

The Biomaker projects have been funded from a variety of sources, starting with support for mini-projects by a Strategic Research Initiative in Synthetic Biology at the University of Cambridge. This was followed by major support (£0.5M) from the BBSRC/EPSRC OpenPlant Synthetic Biology Research Centre, and support from the University of Cambridge Research Policy Committee through the Synthetic Biology Strategic Research Initiative and CamBridgeSens Strategic Research Network. A number of these funding opportunities are ongoing and we actively promote wide participation both within Cambridge and Norwich, and from external partners - including international collaborations at the level of individuals, companies and institutions. In particular, the new Biomaker Challenge has been designed to be easily portable between institutions and open to industrial collaboration, and we invite anyone interested to get in touch.