Calling all biomakers; we challenge you to find technical solutions for biology

This blog post was originally posted on the John Innes Centre Blog on 21.03.2018, and has been reproduced here with permission.

We are today launching the ‘Biomaker Challenge’; a four-month programme, taking place over the summer and challenging teams of people from different disciplines to build low-cost sensors and instruments for biology.

These could be anything from colorimeters to microfluidics and beyond. We’re looking for new, frugal and open source, DIY approaches to biological experiments.

Whether you’re a biologist looking to improve how you work, or pick up some electronics knowledge; an engineer looking to apply your skills and gain experience of practical biology or you’re just curious, we want to hear from you.


Participants will receive a Biomaker Toolkit and a discretionary budget for additional sensors, components, consumables and 3D-printing to help them realise their vision, with the entire package of support worth up to £1,000.

Teams should include at least one member who is a student or member of staff at either the University of Cambridge, John Innes Centre or the Earlham Institute, but external participants are also encouraged to join teams.

The challenge is designed to foster collaboration between institutes, therefore applications from teams composed of participants from multiple places are highly encouraged and will be looked upon favourably by the assessment panel.

Applications close on 11 May 2018.

We will be holding several events in Norwich and Cambridge to provide information about the Biomaker Challenge and help people to develop ideas, discover new collaborations or get involved with projects:

  • 21 March, 7pm – Biomaker Challenge Launch, St Andrews Brewhouse, Norwich
  • 9 April, 2:30-4:30pm – Challenge Info and Mixer Session, Chris Lamb Training Suite, John Innes Centre, Norwich
  • 9 April, 6pm - Pre-Challenge Mixer, Postdoc Centre, 16 Mill Lane, Cambridge
  • 19 April, 6:30pm - Pre-Challenge Mixer, Scholars Café Bar, Union House, University of East Anglia, Norwich

At the end of the challenge, you will be encouraged and expected to exhibit your device at a Biomaker Fayre in Cambridge on 3 November 2018.

Last year 40 interdisciplinary teams showcased their prototypes and prizes were awarded for the best technology, best biology and maker spirit.

One group develop a cell-free biological sensor to detect arsenic in water, another created a low-cost, pressurised liquid chromatography system for protein purification, and a third developed a new, cost-effective way to take a series of macro images and stacking them in order to create one larger, in-focus, image. There are tools available that already do this, but they are very expensive so this project looked at how it could be done cheaper. Encouragingly, the group have since gone on to secure additional funding to take their project further.

We aim for all biomaker projects to be publicly documented with full technical instructions and equipment specifications on This provides anyone around the world with the ability to replicate or adapt what our groups have done, boosting the reach and impact their ideas can have.

Norwich biomakers

There is a Norwich hub for biomaker activities; the Norwich Biomakers meetup group, which brings together a variety of people interested in biology, design, technology, engineering, electronics, software, art and more, to learn from each other about the latest technologies and science advances.

Established in September 2017, the group organises monthly themed events and gives access to a network of nearly 140 biomakers with a broad range of expertise.

Whether biology provides the question, the solution or the inspiration, as an interdisciplinary group we can explore together to generate and share new ideas and skills, find solutions, form collaborations and most importantly, have fun.

Despite only being established for 6 months, we have already seen 3 new collaborations established between researchers on the Norwich Research Park and external people with, for example, electronics expertise, on bioelectricity projects.

We’ve also enjoyed a series of talks at these events from prestigious speakers from the University of East Anglia, as well as from the John Innes Centre and have at least 2 events, each month planned between now and July.

We are always open to new members, check out our online group to find out more and register.

The Biomaker Challenge is administered by the BBSRC/EPSRC-funded OpenPlant Synthetic Biology Research Centre and the Cambridge University Synthetic Biology Strategic Research Initiative.

Norwich Biomakers is supported by OpenPlant SBRC and Innovation New Anglia through the European Regional Development Fund.

DIY macrophotography and embracing the challenge of video documentation


Dr Jennifer Deegan has been awarded an OpenPlant Fund grant to develop teaching materials to enable others to build duplicates of her focus stacking photography setup, and to capture images that can be used for teaching and publications in plant sciences. We caught up with her to find out what she has been up to and how her project is progressing.

Full details of her project can be found on the website, and her full project portfolio is at

Jennifer, please can you give a brief overview of your project?

Jennifer Deegan: The project follows on from my Biomaker 2017 project to build a low budget DIY Focus stacking photography system. The system takes photographs of tiny plant specimens about 2mm across, with the entire specimen in focus.

 An image of a gametophyte fern, captured using the DIY Focus stacking photography system

An image of a gametophyte fern, captured using the DIY Focus stacking photography system

In the past it was not possible to take photographs of such tiny specimens and have them fully in focus. This was because single images taken at high magnification had only a very shallow depth of field. With this new technique we take about 40 photographs of a tiny specimen, with the camera moving progressively towards the subject. Then all of the focused parts of the images are cut out and amalgamated together into one fully focused image.

Commercial systems are available to do this, but they are very expensive. The more affordable ones only move the camera in increments of 2 micrometres. This is not small enough for use at very high magnification. Our system is very cheap and can moved in increments down to about 1/128th of a micrometre.

 The DIY Focus stacking photography system

The DIY Focus stacking photography system

As part of this OpenPlant project we have two goals:

  • Document the construction of the focus stacking system so that others can copy it.
  • Use the system to take plant photos that have never before been possible. These photos will then be made available for plant science teaching and text books.



What inspired the project?

JD: I have always been frustrated that there are no great photos of fern gametophytes anywhere. Fern gametophytes have a very interesting planar heart shaped structure that is brought about by a tightly choreographed series of cell divisions. In the literature they are usually drawn by hand, because they are too small to be photographed in full focus. During my career break to raise my son, I have been working at home as a volunteer, to try to build a system that can take good, full focus, high magnification photographs of these structures.

What has been your favourite aspect of the project so far?

JD: The judges asked me to document my system using videos rather than just in writing. This threw me for a loop initially as I have never made video and didn't have the equipment. However, I have managed to cobble a system together, and am loving my new craft. The time, nuance and attention to detail that is needed to make a short video is amazing. The photo below shows the many photo, video and sound files that I had to record and line up in order to create one short video.  I'm now the proud owner of a YouTube channel. (You can visit it, and the other documentation on GitHub and Hackster via

 Editing videos that explain how the focus stacking system works

Editing videos that explain how the focus stacking system works

What are the biggest challenges you have come across?

JD: There have been a lot of challenges, particularly with the transition from written documentation to video.

The biggest problem is that my laptop is ten years old and is a bit slow for editing video. It cannot play my videos at full speed, so I have to upload them to YouTube between editing session to see what they look like. Saving the files out for upload to YouTube takes 2.5 hours for each video, so it is a slow process.

 The DSLR filming the focus stacking setup, with decoy camera body in place

The DSLR filming the focus stacking setup, with decoy camera body in place

One of my funniest solved problems is that my DSLR is the only camera that I have that can record video, but it also has to appear in the videos. I got around this problem by putting my 27-year-old film SLR as a body double in the videos. The photo to the right shows my DSLR filming the focus stacking setup, with decoy camera body in place. It’s great fun editing the sound of the camera shutter into the finished video.

My other challenge is making these rather technical videos engaging to watch. There is a definite risk of them coming over as a bit dry, and so I try to keep them short and make the images interesting. I think that if I can improve my editing equipment at some point, I could make my videos much more engaging.

I’m really enjoying making educational videos and would like to keep doing this work after the end of the OpenPlant grant. I’ve been in touch with the University Public Engagement Office, who have been very helpful, and I’m hoping to learn some tips from them.

You have been awarded both a Biomaker Challenge and OpenPlant Fund grant. How have these enabled the development of the project?

JD: My work absolutely could not have been done without these grants. Most of the work has been done through collaboration, volunteer labour, and home engineering. However, the grants paid for the microscope objectives. Without these amazing lenses, I could not have done the work.

How do you feel the project is progressing?

JD: I think it's going very well. I have four good videos already online, and a lot of written documentation. I have registered a new domain ( as a central doorway to all of the material, and I still have lots of ideas for other videos to make.

Two out of three of my lenses have arrived and I am looking forward to taking some great photos. My Utricularia gibba (bladderwort) plants are growing well in their casserole dish. Utricularia gibba is a small, carnivorous aquatic plant that develops traps to capture its prey. They are being studied by my collaborator Christopher Whitewoods at the John Innes Centre and I have already taken my first few photos of them, as the new traps develop. The traps have a beautiful structure, and as an aquatic plant, will be a great challenge to photograph.

I hope soon also to visit the Sainsbury Laboratory in Cambridge to photograph the trichome mutant phenotypes in Arabidopsis thaliana, belonging to my collaborator Aleksandr Gavrin. I really look forward to the challenge of photographing trichomes, that will have other trichomes behind to confuse my software.

I have also just sewn a new batch of fern spores and those plants will be a real treat to photograph when the time comes.

What are the future opportunities to take this project forward?

JD: One of the biggest pitfalls for photographers is that they become so fascinated by the stream of newer and better camera equipment, that they forget to actually take any photos. I think that in the next couple of years, it's very important that I actually take the time to take some photographs. With this new technology that I have built, and with the opportunity of my volunteer labour, these will add hugely to the body of research knowledge.


Jennifer's project is also documented on Github:

Eleven projects pitch for funding from the OpenPlant Fund

 Aleksandr Gavrin pitching his proposal.

Aleksandr Gavrin pitching his proposal.

Friday 1 December 2017, Norwich, was the day of the pitches for the 5th round of OpenPlant Fund proposals – and what an exciting set of proposals they were. Eleven proposals were pitched, ranging from development of plant tools and methods, to cell-free protein production, software and hardware development, training, and development of resources for schools in Ghana.

The OpenPlant Fund is rapidly building a dynamic community of early career plant synthetic biologists. The Fund has awarded over 60 micro-grants between 2015 and 2017 to projects facilitating exchange between University of Cambridge, the John Innes Institute and Earlham Institute in Norwich and a range of external collaborators for the development of open technologies and responsible innovation in the context of synthetic biology. Through these awards, OpenPlant aims to promote plant synthetic biology as an interdisciplinary field. This latest round of “high quality, innovative and novel ideas” – as judge Richard Hammond of Cambridge Consultants put it – highlights the engagement, motivation and drive the is present within the local community. More information on the Fund can be found at and documentation of OpenPlant Fund projects can be found at

 Fern gametophyte photographed by Dr Jennifer Deegan using her focus stacking photography platform. More information, images and project documentation can be found through

Fern gametophyte photographed by Dr Jennifer Deegan using her focus stacking photography platform. More information, images and project documentation can be found through

Tools for plant synthetic biology

The first talk, coming to us via skype, pitched for funding to further develop a focus stacking photography platform for teaching and publication in plant sciences. Impressive images of fern gametophytes showed the current scope of the platform developed through the Biomaker Challenge. Presenter Jennifer Deegan (University of Cambridge) made full use of skype by demonstrating the hardware setup, explaining how it would be further developed to expand its scope, and how it would be adapted to build a cheap system for schools.

Next up, Aleksandr Gavrin (Sainsbury Laboratory, University of Cambridge) presented a proposal to make stable transgenic Medicago truncatula lines in which actin is tagged with a reporter gene as a tool for legume researchers. In another legume-focused project, Abhimanyu Sarkar (John Innes Centre) proposed to establish a transformation system for the orphan crop Grass-pea. While there were some challenging legal questions surrounding the shareability of the system, the judges recognised the urgent need for new developments in transformation.

 Image by  Pablo Ramdohr , shared under licence  CC BY 2.0

Image by Pablo Ramdohr, shared under licence CC BY 2.0

Cell-free biology

Proposing to compare cell-free and plant expression systems for protein expression, Susan Duncan (Earlham Institute) pitched a project that would analyse synthesis of proteins, focussing specifically on transcription factors. New collaborations between groups in Norwich and Cambridge will provide Susan with a variety of transcription factors to test.

In a related, but “very independent” project, Quentin Dudley (Earlham Institute) proposed to compare protein synthesis in two different cell-free systems, E.coli and wheat germ lysates. The project aims to gather data on yield vs cost of the two systems. He extended on open invitation for people to ask him “can you try my protein”. So, get in touch if you’d like your plant protein to be tested in Quentin’s cell-free systems.

The third cell-free proposal came in via skype, with Clayton Rabideau (University of Cambridge) rubbing the sleep from his eyes to pitch from the US in the early morning hours. Clayton pitched for funding to develop a hardware system called Open-Cell, using machine learning together with microfluidics-based cell-free screening assay technology for screening of enzyme activity.

Computation and training

A third theme that came out through the pitches, was the need for computation, software development and training. Chris Penfold (University of Cambridge), who had arrived straight off a plane from Venice, proposed an ambitious project to develop a suite of computational tools to simulate large gene regulatory networks in plants and mammals. These tools aim to improve rational design and predictability in synthetic biology.


Jan Sklenar (The Sainsbury Laboratory, Norwich) presented a proposal to bring together proteomics experts and bioinformaticists with expertise in R software. To do this, the group propose a series of workshops for knowledge exchange and training to help both disciplines understand each other. Following these workshops, the team will work together to integrate the ‘R for Proteomics’ package, developed at the University of Cambridge, into Norwich proteomics workflows and further develop the software suite. Jan’s driving motivation for the project is to “be more efficient” and require “less manual interference” for proteomics analysis.

A final computational project was pitched by Aaron Bostrom (Earlham Institute) who talked about mutant worms and Raspberry Pi’s in a proposal to develop a training programme designed around sensing hardware for data collection and machine learning for plant synthetic biology projects.

 An artistic representation of a plant-microbial fuel cell, submitted in Paolo Bombelli's proposal

An artistic representation of a plant-microbial fuel cell, submitted in Paolo Bombelli's proposal

International activities

Two energetic presenters pitched projects focussed on engaging directly with an international group. Paolo “the plant electrician” Bombelli (University of Cambridge) pitched for match-funding to enable him to run an international biodesign competition for the development of prototypes for a plant-microbial fuel cell to be used in remote jungle regions as an environmentally friendly power supply for a sensor and camera-trap to be used by Zoologists.

Waving his hands as he introduced himself, PhD student Hans Pfalgraz (University of East Anglia and John Innes Centre) proposed a project, working with Kumasi Hive innovation hub and the Lab_13 Ghana practical science education project, to take inspiration from previous OpenPlant projects and develop open source practical teaching activities, testing these in Ghana and then making more widely available for schools in other low-resource settings.

What the judges say

“This was a great event and I thoroughly enjoyed it. It felt like we visited all four corners of science in a couple of hours. The proposals were of a high standard and well presented with some fascinating new ideas to understand and discuss. Well done to all involved.’

— Richard Hammond, Technology Director and Head of Synthetic Biology at Cambridge Consultants

“It was a great day, very good science, creativity and a warm welcome. Thanks for the invite!

— Ward Hills, CEO at OpenIOLabs

“We heard a number of compelling and original ideas, the majority being led by early career researchers. It was particularly impressive to see so many new collaborations and networks being built, both between the Open Plant Research Institutes and with external partners.

— Dr Nicola Patron, Synthetic Biology Group Leader, Earlham Institute

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


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.


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


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

IMG_6246 (1).JPG

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 

group31 (1).jpg

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.


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.


  • 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 or on +44 (0)1603 450267.

 More information at:

More information at: platform for Biomaker projects

We have set up a new platform for Biomaker projects on 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.

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 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 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

Open Technology Week 2017 Poster_3.jpg

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.


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.


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.


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.