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
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.
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 (firstname.lastname@example.org).
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Opportunities for collaboration
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.
Synthetic Biology meets real world instrumentation
The Biomaker programme provides funding for interdisciplinary team-based projects at the intersection of electronics, 3D printing, sensor technology, low cost DIY instrumentation and biology - and policy workshops and outreach events. These projects aim to build open technologies and promote development of research skills and collaborations. They tap into existing open standards and a rich ecosystem of resources for microcontrollers, first established to simplify programming and physical computing for designers, artists and scientists. These resources provide a simple environment for biologists to learn programming and hardware skills, and develop real-world laboratory tools. Further, the Biomaker projects provide a direct route for physical scientists and engineers to get hands-on experience with biological systems.
We have organised annual Biomaker Challenges for the last three years (2017-2019) for interdisciplinary teams to build low-cost instruments for biology. 88 projects have been funded that involved around 300 participants from Cambridge, Norwich and beyond. This complements the OpenPlant Fund, which has funded a total of 71 interdisciplinary and cross-institute projects.
We adopted the visual programming interface XOD to tackle some of the bottlenecks and difficulties that non-programmers face when building electronics, and implemented a training programme aimed at teaching basic hardware and software for scientists. We’ve organise hands-on workshops to encourage the development of new biological technologies through the OpenPlant Fund.
A full list of about 150 completed projects can be found here.
OpenPlant and Biomaker are working with Global Challenges Research Funds and African partners to develop resources for open and accessible teaching resources for engineering biology. We have supported a workshop on Practical Synthetic Biology: fast, frugal and open technologies for education and sustainable development in Africa, resulting in the Bakubung Report. OpenPlant has supported the JR Biotek Foundation Workshops in Cambridge and the Benin Republic, attended by African researchers. Biomaker is working with partners at the Kumasi Hive in Ghana, Mansoura University, Egypt; University of Pretoria, South Africa; Bahir Dar University, Ethiopia and University of Adelaide, Australia to develop international Biomaker Challenges.
As part of the recruitment of international teams, we have established a web-based platform for documentation of Biomaker projects at https://www.hackster.io/biomaker/.
Cafe Synthetique is an informal get-together for people interested in synthetic biology and construction and interrogation of reprogrammed biological systems. Evening discussion meetings are held monthly at the Panton Arms pub in Cambridge. Details of these and other synthetic biology related events can be found at the Meetup site:
SynBio SRI Fund
The SynBio Fund supported eighteen innovative, open and interdisciplinary projects relevant to Synthetic Biology over 2015-16. The aim of the fund was to promote the development of Synthetic Biology as an interdisciplinary field at the University of Cambridge.
The OpenPlant Fund supports innovative, open and interdisciplinary projects relevant to plant Synthetic Biology. The fund facilitates exchange between the University of Cambridge, the John Innes Centre, and the Earlham Institute for the development of open technologies and responsible innovation.