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2018 Open Technology Workshop

Join us in celebrating and showcasing open technologies in research and education. The day-long event will consist of a morning of talks on everything from open technology for wildlife conservation to hackathons in Zimbabwe, followed by a Biomaker Fayre in the afternoon where this year's Biomaker Challenge teams, as well as makers from the community, will exhibit their open technology projects.

OpenTechWebpage

 

SCHEDULE

9:00-9:30 Check-in 

9:30-9:45 Welcome

Jim Haseloff (University of Cambridge)

9:45-10:20 “Open tools for animal conservation”

Alasdair Davies (Shuttleworth Fellow)  & Paolo Bombelli (Department of Biochemistry, University of Cambridge)

 10:20-10:55 “Hacking open source 3D printers to make better solar cells”

Grey Christoforo (Department of Physics, University of Oxford)

 11:00-11:30 Coffee break

 11:30-12:00 “Open Cell: building a critical mass for biotechnology”

Helene Steiner (Co-founder & Director of Open Cell, Co-founder & CCO of Cell-Free Technology)

 12:00-12:30 “600 below to 400 above: science with Raspberry Pis”

Richard Hayler (Senior Programme Manager, Community and Development, Raspberry Pi)

 12:30-13:00 “Open instrumentation for Africa: microscopes, measurements, and more”

Julian Stirling (Department of Physics, University of Bath)

 13:00-14:00 Lunch

 14:00-16:00 Biomaker Fayre

 16:00-17:00 Prize giving & drinks reception 

 

BIOMAKER FAYRE EXHIBITS

*2018 Biomaker Challenge team

 

A1- Citizen Science with Raspberry Pi Richard Hayler

Since its launch in 2012, over 20 million Pis have been sold. Many of these are used by scientists of all ages, and several hardware products that use the Pi as the core of a scientific instrument have been developed and produced.

A2 - MicrobeMeter (Humane Technologies) Kalesh Sasidharan, Orkun Soyer 

Which microbes surround you? Under what conditions can they grow? What is the fastest growing microbe? These and many other research questions in microbiology, synthetic biology, and biotechnology require growing microbes and monitoring their growth. We will demonstrate MicrobeMeter – a high-resolution, do-it-yourself and affordable photometer developed by Humane Technologies Limited for monitoring of microbial growth. It can be used in any environment including research laboratories, schools, in the field and even your home. 

A3 - Building a Raspberry Pi Multispectral Camera Boyuan Xiao

Gauging plant heath by using a R-Pi and a NoIR/RGB camera to take images in both the visible and near infra-red spectrum.

A4 - A Cartesian Coordinate Robot for Dispensing Fruit Fly Food Matt Wayland, Matthias Landgraf

The fruit fly, Drosophila melanogaster, continues to be one of the most widely used model organisms in biomedical research. Though chosen for its ease of husbandry, maintaining large numbers of stocks of fruit flies, as done by many laboratories, is labour-intensive. One task which lends itself to automation is the production of the vials of food in which the flies are reared. Fly facilities typically have to generate several thousand vials of fly food each week to sustain their fly stocks. The system presented here combines a cartesian coordinate robot with a peristaltic pump. The design of the robot is based on an open hardware CNC (computer numerical control) machine, and uses belt and pulley actuators for the X and Y axes, and a leadscrew actuator for the Z axis. CNC motion and operation of the peristaltic pump are controlled by Grbl, an open source, embedded, G-code parser. Grbl is written in optimized C and runs directly on an Arduino. A Raspberry Pi is used to generate and stream G-code instructions to Grbl. A touch screen on the Raspberry Pi provides a graphical user interface to the system. Whilst the robot was built for the express purpose of filling vials of fly food, it could potentially be used for other liquid handling tasks in the laboratory.

*A5 - Temperature controlled container for sample transportation Dean Kos, Viola Introini

We aim to develop a temperature controlled container that can be used to safely transport sensitive samples with a conventional mail service. We plan to integrate a temperature control system in a special container of the size of a small parcel that is reliable and reusable, and can maintain small samples in a monitored environment throughout the shipping. 

*A6 - Automated water irrigation, lighting and monitoring system for plant growth Cornelius Bausch, Nicola Pellicciotta, Evelyn Hamilton, Roberta Langranco, Alessio Caciagli

We aim to build a Raspberry Pi based self-maintaining plant growing system. It will consist of several sensors in order to monitor humidity, temperature, light conditions and level of water in the reservoir. Additionally, a webcam takes images. All information will be shared on a web server for remote monitoring.

*A7 - Agarose device to generate and study an in vitro embryonic model system Tatiana Subkhankulova, Fergus Riche, Vikas Trivedi

Early stage embryonic development is characterised by a series of drastic and rapid remodelling events which are of interest to scientists, engineers and doctors alike. We have developed a tool to image these events occurring in a model developmental system - gastruloids. These three dimensional aggregates of mouse Embryonic Stem Cells offer many advantages for research, being simple to generate and offering flexibility . Our tool, which is simple to manufacture and assemble, combines the flexibility of additive manufacture with  the precision of mass produced components to allow researchers to make wells in agarose suitable for both cell culture and live imaging.

 A8 - The DaisyDriver: A Flexible Aid for Automation in Science Fergus Riche, Louis Kaplan

Automation transformed the way that industry was able to produce goods for market. Incorporating automation into scientific practice will allow us to overcome many of the limitations that are commonplace in scientific experiments, especially in developing nations. Inspired by the work of Waterscope (www.waterscope.org), who are helping make safe water available in Tanzania using a low cost 3D printed microscope, we designed a motor controller to make automating experiments and tests easy. The DaisyDriver is a motor controller with built-in networking, meaning that its capabilities can be expanded as necessary: simply by connecting two or more units together.

*B1 - Wearable biosensor for monitoring vaginal discharge Tommaso Busolo, Giulia Tomasello, James Che, Michael Calabrese

This project stems from the idea of developing an inconspicuous, low-cost wearable biosensor aimed at monitoring physiological markers of infection, such as lactate and pH, in vaginal secretions. On one hand, this will provide insight into what normal and abnormal physiology may be for individual women. On the other, we hope this will provide new insight into the underlying biological processes for research purposes.

*B2 - The Oscillostat: evolution under temporally-controlled selection Om Patange, Jarrod Shilts

We propose to build a low-cost, continuous culture apparatus with temporally modulated environments for experimental evolution. We will do this by expanding on existing designs for turbidostats, devices that maintain a constant density of microbial cultures. Our device, the Oscillostat, will switch between inputs to generate user-specified selective pressures of defined frequencies and amplitudes.

*B3 - Open bioreactor for local enzyme manufacturing Jenny Molloy, Juan Mosquera, Anna Kuroshchenkova, Danny Ward, Alexander Kutschera, Pawel Mikulski

We built an open source, bench top, batch bioreactor to optimise yield of enzymes producing recombinant proteins for molecular biology such as Taq polymerase or for cell-free extract production. This builds on existing open source projects to further reduce the cost of components and we paid particular attention to their global accessibility with the goal of making these devices easier to build and maintain for a wider range of users in resource-constrained universities, companies and biomaker spaces.

B4 - Biomakespace Jenny Molloy

Biomakespace is Cambridge’s first community based, open access biology and prototyping space, on the Cambridge Biomedical Campus. We are a community of scientists, engineers, technologists, entrepreneurs, teachers, artists and members of the public interested in engineering with biology. Biomakespace provides members with affordable access to a well equipped lab and prototyping space as well as to training and social events.

*B5 - Visual programming for Biomakers Carlos Lugo, Marco Aita, Alice Minotto

We plan to develop a short, engaging tutorial that will introduce the principles of visual programming to individuals who may have little familiarity or confidence with electronics or scientific computing. We will create a hands-on learning experience consisting of a set of example problems and solutions tailored to be of interest for individuals working in experimental biology/plant sciences.

B6 - Biomaker Winter Challenge Jim Haseloff

*B7 - Improving dual-view imaging in a custom-built light sheet microscope Stephanie Hoehn, Hannah Sleath, Rashid Khashiev, Francesco Boselli, Karen Lee

We previously constructed a light sheet fluorescence microscope (LSFM) for gentle long-term time lapse imaging of living samples including green micro-algae (Höhn et al.), aquatic carnivorous plants (Lee et al.) and developing frog eggs (Boselli et al.). Our original LSFM setup was based on the OpenSPIM (openspim.org) with some modifications [1, 2]. With generous support from the OpenPlant Fund we subsequently added a second detection objective and camera to enable dual-view imaging.

The Objectives of this proposal are to improve dual-view imaging by optimising the hardware parts aligning the two cameras and the software that controls them, to improve bright field imaging by adding stepless intensity control and integrating the control into the acquisition software and to improve multi-view imaging by designing more stable sample holders. Our designs will be made publicly available through openspim.org and will benefit a wide community of scientists using light sheet microscopes.

*B8 - Spectre: palm-sized spectrophotometer Feng Geng, Xiaoyu Chen, Jimmy Chen, Boon Lim

Biosensors detect and convert analytes into detectable signals via biological systems. Using synthetic biology technologies, bacteria can be engineered into whole-cell biosensors (WCBs) to sense physical and biochemical signals in the environment. On top of their high sensitivity (single-molecule level detection), rapid response (<ms), portability, low cost and simple-usage, one of the biggest advantages of WCBs is in-situ detection, which makes WCBs ideal for real-time environmental and medical surveillance. This project aims to develop a portable, low-cost and miniaturised spectrophotometer to realise the potential of WCBs for remote and on-site application. 

However, the current testing bed of biosensors relies on traditional plate reader which is expensive and non-mobile, thus limiting the potential of on-site and real-time detections. This project aims to solve this problem by developing a portable, low-cost and miniaturised spectrophotometer to realise the full potential of WCBs for remote and on-site application.

*C1 - LyseeFlask Indu Santhanagopalan, Kartika Shetty

LyseeFlask will help lyse bacterial cells in a regular shaker-incubator and carry out immobilised ion affinity chromatography. With success, the project would reduce dependency on high-wattage instruments like centrifuges, sonicators and French press. We also plan to immobilise metal ions in LyseeFlask to make it a conduit for affinity purification of His-tagged proteins. We believe that the LyseeFlask strategy could be easily modified for high-throughput purification of multiple proteins.

 

CALL FOR EXHIBITORS!

The fayre will highlight projects by 14 teams participating in this year's Biomaker Challenge - a four month programme challenging interdisciplinary teams to build low-cost, DIY instrumentation for biology. For more information, visit www.biomaker.org.

If you have an interesting project using open technologies, created as part of the Biomaker Challenge or independently, you are invited to exhibit it at the Biomaker Fayre during Open Technology Week!

  • Register your project 
  • Complete a risk assessment (Please dowload and fill in the template and upload back to the folder renamed with the title of your project by October 15. Null returns are required and the template allows for this.)
  • Prepare a PDF A3 poster and upload to the shared folder. We will print it for you on good quality card! 


Please email Alex at  with any questions.

About

The Synthetic Biology Strategic Research Initiative provides a hub for anyone interested in Synthetic Biology at the University of Cambridge, as well as commercial partners and external collaborators.