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 Hackster.io. 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.

Synthetic Biology and the Senses at Cambridge Science Festival, March 2018.

The morning shift: Some of the Cambridge Science Festival 2018 team ready for doors open.

For the third year in a row, OpenPlant teamed up with the SAW Trust and Cambridge Synthetic Biology SRI to deliver a variety of activities on our interactive stand at the Cambridge Science Festival.

While braving the icy ‘pest from the west’ we explored some of the natural products made by plants with those who dared to venture out in the chilly weather. In keeping with this year’s festival theme ‘making sense of our world’, our ‘Synbio and the senses’ stand enabled participants to extract their own plant pigment, learn how plants make proteins and meet the one and only DNA Dave!

Extracting anthocyanin from red cabbage at the Cambridge Science Festival

The main activity of the stall involved visitors extracting the anthocyanin pigments from red cabbage, getting hands on with a natural pigment and investigating its sensitivity to pH levels. Children and adults alike, seemed to have great fun pipetting out their cabbage juice, acid (lemon juice) and alkaline (bicarbonate of soda solution) onto discs of filter paper to create their own artworks.

Visitors were excited to take home a worksheet explaining the science behind the pigments, and giving instructions for doing their own extractions and experiments at home. You can find the worksheet here.

Colour Bio-factories - using genetic engineering to boost existing pathways within plants to produce natural pigments.

In addition to the pigment extraction, visitors could learn about how researchers in Cathie Martins’ lab at the John Innes Centre are now producing these anthocyanin pigments in plants, using genetic engineering to boost a native pathway. At present there is only one natural blue pigment that is available for food colouring, which is produced from an alga called spirulina. However this blue is not very strong or stable in colour. Therefore, most blue food colourants are chemically produced synthetic compounds. The research conducted by Dr Ingo Appelhagen  in the Martin lab is enabling the discovery of new, more stable, anthocyanins found in nature and the use of plant cell cultures  to produce these more stable forms in larger amounts so that they could be used as non-synthetic colourings. They can generate a range of colours, including bright blues.

Visitors were also able to have a go at putting together their own synthetic biology plant system with the use of an interactive jigsaw game in which they chose a plant species to work with, a site or organ of the plant where they could make something happen, and a signal that would cause it to happen. To complete the game, they could then learn how proteins are made from the instructions in DNA with the help of DNA Dave! DNA Dave is a robot whose mechanics describe the processes of “transcription” and “translation” through which DNA is copied, then read and translated into a protein. As with previous events, DNA Dave was an absolute hit with all the visitors, including his namesake – Sir David Attenborough! Participants were even given the chance to design their own protein that could be used by DNA Dave.

A young visitor to the Cambridge Science Festival designs her own protein.

DNA Dave helps to explain the production of proteins.

With visitor numbers reaching 1600 in our marquee alone, the day was a great success with lots of enthusiastic individuals - if a little nippy! A big thank you to all our volunteers from the University of Cambridge and the John Innes Centre, Norwich, who helped on the day and did a great job!

Biomakespace opens its doors to new members!

Biomakespace in Cambridge is a community based, open access biology and prototyping space, which aims to contribute to awareness, knowledge and innovation in engineering with biology.

Providing members with affordable access to a well-equipped lab space, as well as training and social events, the project aims to build a community of scientists, engineers, technologists, entrepreneurs, teachers, artists and members of the public, keen to work at the interface of biology and engineering.

A dedicated team have been refurbishing the lab space since September 2016 and it's doors are now open to new membership applications! 

Check out the membership page for more details

Read more in this Cambridge Network blog post

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 biomaker.org website.

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

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

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 www.chlorophyllosophy.uk)

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

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 (www.chlorophyllosophy.uk) 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: https://github.com/BioMakers/Gametophyte-Fern-photography-2018/blob/master/README.md

[Closing March 6 - April 10] Several lectureship opportunities at Edinburgh University

Lecturer or Senior Lecturer in Synthetic Biology (vacancy ref: 042732)

We seek an excellent scientist and inspiring teacher who uses synthetic biology methods in research programmes such as genome engineering, biotechnology, metabolic engineering, genetic circuit design and engineering (both in vivo and cell free), bio-sensing, multi-cellularity and tissue engineering, regenerative medicine, novel vaccine development or addresses key questions in molecular or cell biology. The Edinburgh Genome Foundry’s facilities for automated DNA assembly can support large-scale synthetic biology and synthetic genomics research and we would be particularly enthusiastic about research programmes that took advantage of these capabilities.

Closing date – March 22nd

Contact – Prof Susan Rosser (Susan.Rosser@ed.ac.uk)

Lecturer in Biological Mass Spectrometry (vacancy ref: 042692)

We seek an excellent scientist and inspiring teacher who applies mass spectrometry (MS) in innovative ways to tackle major challenges in biology. We are looking for researcher who is addressing key questions in areas such as cell biology, structural biology, immunology, microbiology, biotechnology or systems biology, by exploiting the unique sensitivity, accuracy and resolving power of modern and emerging MS techniques.

Closing date – April 5th 2018

Contact – Prof Paul Barlow (Paul.Barlow@ed.ac.uk)

Lecturer in Computational Biology (vacancy ref: 042673)

We seek an excellent scientist and inspiring teacher who uses and develops computational and modelling techniques to address key questions in biology. We welcome applications from researchers in all areas of computational biology, and we are particularly looking for those working in the following fields: metabolism, such as the application of flux balance analysis and the analysis and interpretation of data from metabolomics and fluxomics experiments; multi-scale modelling of biological systems, including formal modelling techniques and stochastic modelling; and data science approaches to biological research, including the analysis of data from next generation sequencing.

Closing Date - 13th March 2018

Contact – Prof Peter Swain or Prof Guido Sanguinetti (Peter.swain@ed.ac.uk or gsanguin@inf.ed.ac.uk)

Lecturer in Stem cell Biology (vacancy ref 042667)

We seek an excellent scientist and inspiring teacher who addresses key questions in stem cell biology or developmental biology that are directly relevant to stem cell or regenerative biology. We particularly encourage applications from candidates who employ single cell or synthetic approaches

Closing Date – April 10th

Contact – Prof Donal O’Carroll Donal.ocarroll@ed.ac.uk

Lecturer in Molecular Crop Science (vacancy ref: 042668)

We seek a creative scientist and inspiring teacher who applies molecular approaches to address important fundamental and translational questions in plant biology that are relevant to crop improvement and food security.

Closing Date – March 15th

Contact – Prof Andrew Hudson (Andrew.hudson@ed.ac.uk)

Lectureship in Biochemistry (vacancy ref 042671)

This four-year lectureship position offers an outstanding opportunity to develop an independent teaching and research programme. We seek an excellent scientist and inspiring teacher to join a group of successful scientists with teaching and research interests across RNA and cell biology, synthetic biology, systems biology, biochemistry and biotechnology. At Edinburgh we emphasise cross-disciplinary thinking in a collaborative and well-supported environment. You will benefit from this to build your own portfolio of research and scholarship. You will make an important contribution to the development and delivery of high-quality and inspirational undergraduate and postgraduate teaching, including the opportunity to develop eLearning and on-line education initiatives. You will have a PhD in a relevant area of biology or chemistry and a published record of research, along with a successful track record of developing innovative and engaging teaching.

Closing Date – March 6

Contact – Prof Paul Barlow (paul.barlow@ed.ac.uk)

For all roles, please apply online at vacancies.ed.ac.uk

Eleven projects pitch for funding from the OpenPlant Fund

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 www.openplant.org/fund and documentation of OpenPlant Fund projects can be found at www.biomaker.org.

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

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

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

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

New report from the OpenPlant IP Working Group: Towards an Open Material Transfer Agreement

View the full report >>

The OpenPlant Intellectual Property (IP) Working Group was formed to examine IP norms and policies that impede innovation in plant synthetic biology. The result was the development of the Open Material Transfer Agreement (OpenMTA), a legal tool for sharing DNA parts and other biological materials that allows IP-free sharing of foundational tools while promoting the scaling and commercialisation of novel advanced technologies.

OpenPlant is a collaborative initiative between the University of Cambridge, the John Innes Centre and the Earlham Institute in Norwich. It is a synthetic biology research centre focused on the development of open technologies for plant synthetic biology. As part of this initiative, the OpenPlant Intellectual Property (IP) Working Group was formed to examine current IP norms and policies that impede innovation in plant synthetic biology and develop pragmatic solutions.

OpenPlant is building a collectionof promoters to drive expression of fluorescent markers in the liverwort Marchantia polymorpha which will be shared with the plant synthetic biology community. Image: Bernardo Pollak, Haseloff Lab, University of Cambridge

The Working Group met at the University of Cambridge on 30 July 2015 to solicit input on the design specifications for an open material transfer agreement (OpenMTA), a legal tool that complements the BioBrick® Public Agreement and supports the sharing of DNA components as tangible material. The second aim was to gather and prioritise actionable goals for creating and sustaining an international platform of open technologies for plant synthetic biology.

This report provides background and context for our discussions then summarises the observations of the 23 participants, who included researchers, technical experts, and legal practitioners from academic, industry, and non-profit organisations.

“We believe steps to facilitate exchange of DNA parts and tools will substantially speed the take-up of new technologies in plant synthetic biology.”

The OpenPlant IP Working Group continued discussions through monthly calls and drafted several comment pieces and conference presentations. After extensive consultation, the text of the OpenMTA Master Agreement is published, initial signatories are invited and the first transfers of materials are beginning to take place, including transfer of bacterial DNA parts from Stanford University to the J Craig Venter Institute. Work continues to address the other issues identified in this report in the context of sharing OpenPlant-derived tools and technologies.

The authors welcome feedback on this report and invite suggestions for concrete actions enabling the creation and maintenance of platforms for sharing open biotechnologies. 

For more information on the OpenMTA, see http://openmta.org

[Closes 22 Mar 2018] Vacancy for Lecturer or Senior Lecturer in Synthetic Biology at University of Edinburgh

Vacancy: Lecturer or Senior Lecturer in Synthetic Biology

We seek an excellent scientist and inspiring teacher who uses synthetic biology methods in research programmes such as genome engineering, biotechnology, metabolic engineering, genetic circuit design and engineering (both in vivo and cell free), bio-sensing, multi-cellularity and tissue engineering, regenerative medicine, novel vaccine development or addresses key questions in molecular or cell biology. The Edinburgh Genome Foundry’s facilities for automated DNA assembly can support large-scale synthetic biology and synthetic genomics research and we would be particularly enthusiastic about research programmes that took advantage of these capabilities.

You will have the ability, enthusiasm and breadth of vision required to be a future leader in this rapidly moving field. You will pursue an independent research programme, working collaboratively and leading a team. You must have an established track record of relevant publications and the potential to win future investment in research, and will be expected to engage with both commercial and public research users and funders. You will be enthusiastic about teaching and student-centred learning for both undergraduate and postgraduate students.

The University of Edinburgh is a vibrant, research-driven community offering opportunities to work with internationally leading academics whose visions are shaping tomorrow’s world. The School of Biological Sciences is one of the UK’s largest and most highly rated life sciences departments, providing an innovative environment for research and teaching with a strong emphasis on interdisciplinary research. SynthSys, the Centre for Synthetic and Systems Biology, is one of the largest groupings of systems and synthetic biologists in the UK with expertise ranging from microbes to mammalian cells working on applications in biotechnology and medicine as well as contributing to foundational and fundamental research. SynthSys is highly multidisciplinary with members from the schools of engineering, informatics, chemistry, physics, social sciences, medicine as well as biological sciences. You will join a team of group leaders working at the interface between molecular cell biology and quantitative science, with strong links in biotechnology.

Informal enquiries: Prof Susan Rosser susan.rosser@ed.ac.uk

This posts are full time and open ended.

Salary: UE08 £39,992 - £47,722 per annum / UE09: £50,618 - £56,950 per annum

Closing Date: Thursday 22nd March 2018 at 5pm (GMT)

To apply: www.vacancies.ed.ac.uk search for #042732

Postdoc representatives sought for University of Cambridge Open Research Working Group

The Open Research Working Group will convene in Lent Term 2018 to define and develop the University’s approach to open research, including open access to publications and open research data. The working group is seeking two postdoc representatives with some background or interest in open research, one from STEM and one from AHSS.

This opportunity may appeal to those working in the open technology area, with OpenPlant or who have received OpenPlant or SynBio Fund support and have some interest in or experience of open research.

Remit of the Working Group

The Open Research Working Group will be convened in the Lent Term 2018 to clarify the University’s needs and expectations on Open Research. The group will define and agree on the University’s stance on Open Research and help shape service, infrastructure and policy developments in response to the Open Research agenda. Broadly speaking, Open Research is taken to mean the overall drive towards sharing (data, method, outputs) of University research, and the changing research and dissemination practices intended to maximise public access to these. Open Research is inclusive of Open Access to research publications and doctoral theses and the processes and planning involved in research data management which can, where appropriate, lead to the sharing of Open Data.

Level of Commitment

The working group is a short-term commitment of 4-5 meetings between Feb and June 2018. It is an excellent opportunity to voice the perspective of postdocs in how the University addresses this important topic, as well as valuable experience for an academic careers.

Contact james.brown@admin.cam.ac.uk if you are interested in this opportunity.

Apply now for eLife Innovation Sprint - bringing cutting-edge technology to open research

The eLife Innovation Sprint is a two-day challenge on 10-11 May 2018 for developers, designers, technologists and researchers to collaboratively prototype innovations that bring cutting-edge technology to open research.

The eLife Innovation Initiative have been working to improve research transparency and accessibility, and accelerate discovery in the life sciences, by developing open-source technologies in collaboration with the wider community. They have heard many excellent ideas for transforming how the latest science is shared, built upon and recognised, and  they want to create a space that would help translate these ideas into action.

By bringing ideators, creators and users together for the Innovation Sprint, they hope to provide space, time and access to diverse skill sets for the community to develop their ideas into prototypes and forge new collaborations.

eLife invite you — whether change maker or web wrangler, UX champion or data tinkerer — to apply to participate in person.

Apply now >>

Applications will close at 9am GMT on March 5 2018, and we aim to communicate the outcome of each application by March 23 2018.

[Closes 16 April] Accepting applications for the 2018 Cold Spring Harbor Laboratory Summer Course in Synthetic Biology

We are now accepting applications for the 2018 Cold Spring Harbor Laboratory Summer Course in Synthetic Biology. We encourage you, your colleagues, and/or your trainees to apply if…

• You are a scientist whose training is well underway (senior graduate student to junior faculty and beyond).
• You are interested in steering your research in a new direction, towards synthetic biology.
• You are interested in a multi-disciplinary approach to biology and bioengineering. We encourage students of all backgrounds, whether the very biological or very theoretical, to apply!
• You work in the field of synthetic biology and are interested in new techniques.

Since the course began in 2013, industry professionals, graduate students, postdocs, science educators, and junior faculty have completed our immersive two-week laboratory class. The Course will focus on how the complexity of biological systems, combined with traditional engineering approaches, results in the emergence of new design principles for synthetic biology. Students will work in teams to learn the practical and theoretical underpinnings of cutting edge research in the area of Synthetic Biology. In addition, students will gain a broad overview of current applications of synthetic biology by interacting with a panel of internationally-recognized speakers from academia and industry during seminars, lab work, social activities.

Scholarships: Several stipend awards are available for applicants who are accepted into the course. Please read details about the available stipend awards at: https://meetings.cshl.edu/sponsors.aspx?course=C-SYNBIO&year=18

In order to be considered for an award, you must specifically reference which one you are eligible for in the Stipend Request section of your application.

• Course dates: July 24 - August 6, 2018
• Application deadline: April 15, 2018
• Application submission information: http://meetings.cshl.edu/courses/2018/c-synbio18.shtml
• Course blog & website: https://cshlsynbio.wordpress.com/

[Closes 28 Feb] Early registration now open for Crossing Kingdoms: an international synthetic biology symposium

Crossing Kingdoms is an international 3 day-event bringing together scientists from the microbial, animal and plant fields to present their results and highlighting how knowledge from these different life forms provide tools for synthetic biology innovations and applications.

Registration for Crossing Kingdoms is now open.

 

Abstract submission

Submissions for oral and poster presentations  are welcome.  To submit a pdf or Word file containing your abstract please complete the electronic submission form here.

List of confirmed speakers:

• Pamela Silver, Harvard University
• Matias Zurbriggen, University of Düsseldorf
• Chang Liu, UC Irvine
• Dan Voytas, University of Minnesota
• Ben Blount, Imperial College
• Sean Cutler, UC Riverside
• Alison Smith, University of Cambridge
• Giles Oldroyd , Sainsbury Laboratory – University of Cambridge
• Anne Osbourn, John Innes Centre

Organisers:

Alain Tissier (Halle) and Philip Wigge (Cambridge).
Supported by the German Ministry of Education and Research (BMBF) and the UK Biotechnology and Biological Sciences Research Council (BBSRC) and ERA-SynBio.

Download the conference poster for your noticeboard

[Closes 12 Mar 2018] OpenPlant and SynBio SRI seek new Coordinator - apply now!

The University of Cambridge is seeking a Co-ordinator for two Synthetic Biology research initiatives. The role-holder would work 50% to support the OpenPlant Synthetic Biology Research Centre and 50% with the Synthetic Biology Strategic Research Initiative (SynBio SRI).

We are seeking a Co-ordinator for two Synthetic Biology research initiatives at the University of Cambridge. The role-holder would work 50% to support the OpenPlant Synthetic Biology Research Centre and 50% with the Synthetic Biology Strategic Research Initiative (SynBio SRI). The purpose of the role is to help develop and implement a strategy that will enable both initiatives to become known leaders in the field and sustainable in the longer term.

OpenPlant (http://openplant.org) is a consortium funded by BBSRC and EPSRC comprising 20 labs spanning the University of Cambridge, John Innes Centre and the Earlham Institute (Norwich). The work of the Research Centre is intended to promote novel research on tools and applied traits for plant synthetic biology, open sharing of foundational technologies, and responsible innovation. The role-holder will work with the OpenPlant Directors and Management Group, including the OpenPlant Project Manager based in Norwich, to co-ordinate a variety of activities within the Research Centre.

The SynBio SRI (http://synbio.cam.ac.uk) aims to catalyse interdisciplinary exchange between engineering, physics, biology and social sciences to advance Synthetic Biology at the University of Cambridge. The role-holder will work with the SRI Co-Chairs and Steering Committee to develop, plan and deliver the SRI's vision and strategy. They will facilitate efforts to promote development of open technologies, build shared resources, and provide a hub for networking and discussion.

Responsibilities will also include co-ordinating seed funding competitions such as the Biomaker Challenge and OpenPlant Fund; organising formal and informal scientific meetings and forums; developing and managing relationships with stakeholders within and external to the University; seeking small and large-scale funding for future activities. The role-holder is additionally responsible for ensuring that synthetic biology activities in Cambridge are actively communicated and promoted, and is supported by the part-time SynBio SRI Events and Communication Co-ordinator.

The successful candidate will have a PhD in a relevant field and knowledge of Synthetic Biology research, policy and practice. They will have the ability to foster relationships with and between academics at all levels in an interdisciplinary context, and build partnerships with companies, funders and policy makers. A successful track record in attracting research funding would be advantageous. Excellent organisational and communications skills are essential, together with proven problem-solving skills and initiative.

 For more information and to apply >>

[Closes 20 Feb 2018] Synthetic Biology Postdoc at Earlham Institute

OpenPlant PI Dr Nicola Patron is looking for a Postdoctoral Research Scientist to work on a European Research Area (ERA) CoBioTech collaborative project based in the Patron Lab at the Earlham Institute. The project will use will use synthetic biology, comparative transcriptomics, metabolic engineering and genome editing/engineering techniques to develop plants and fungi as low-cost, sustainable production platforms for biosynthesis of insect pheromones..

Apply now >>
Closing date 20th February 2018

[Closes 14 March 2018] NSF-USDA-BBSRC Joint Funding Opportunity to Develop Breakthrough Ideas and Enabling Technologies to Advance Crop Breeding and Functional Genomics

The National Science Foundation (NSF) Biological Sciences Directorate (BIO), the U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) and the UK's Biotechnology and Biological Sciences Research Council (BBSRC) have established a joint funding opportunity to support the development of breakthrough technologies that will enable significant advances in crop breeding. This opportunity aims to make high impact changes in the ability to translate basic knowledge of plant genomics to practical outcomes in crops of economic importance to the participating countries.

This NSF-BIO, USDA-NIFA and BBSRC Joint Activity is soliciting Early Concept Grants for Exploratory Research (EAGER) proposals to support development of breakthrough ideas and technologies to speed the development for new crop varieties.

See more information below and at this page >>

There remain significant bottlenecks to improving crop varieties even if new traits or natural variants are identified, such as producing hybrids, understanding recombination, and epigenetic inheritance as examples. Translation of basic knowledge to practical outcomes can be accelerated by key emerging technologies that exploit genomics rapidly and effectively. This EAGER opportunity invites proposals to overcome these barriers to crop breeding in highly innovative and transformative ways. Investigators considering this opportunity should articulate how the enabling technologies would be used to improve crop breeding.

Areas of research that await breakthrough advances and are appropriate for this EAGER opportunity include, but are not limited to, the following:

• Advancing genome editing technology to generate new phenotypes for greater genetic gain
• Achieving reliable and high throughput production of doubled haploids from genotypes that are currently recalcitrant to chromosome doubling to accelerate the breeding process in cereals and other crops
• Controlling and understanding meiotic recombination to tap into inaccessible genetic resources in areas of low recombination and enabling whole genome manipulation
• Modifying epigenetic inheritance to facilitate phenotypic changes related to environmental responses
• Understanding mechanisms of heterosis, thereby generating and exploiting hybrid vigor for crop improvement

For this EAGER opportunity, emphasis should be on developing enabling technologies that will impact crops or model crop systems. Projects that focus solely on sequencing will not be considered. Funded projects relevant to the goals of the International Wheat Yield Partnership (IWYP) will be invited to become IWYP Aligned Projects.

Proposed studies should be potentially transformative and must be considered "high-risk, high-payoff" to achieve the goal of making technological breakthroughs to promote crop breeding. Studies should be compatible with the budget (up to $300,000 for US components and up to £200,000 for UK components) and time limits (2 years) of the EAGER funding mechanism. For collaborative US/UK EAGER projects, BBSRC will fund UK researchers up to £200,000 and NSF or NIFA will fund US researchers up to $300,000 including indirect costs. US only EAGERS are limited to $300,000 total including indirect costs. Further details are provided below for budgetary limits for UK partners. EAGER proposals may originate from US-UK partnerships or from US-only applicants. EAGERs solely involving UK applicants are not permitted. For more information on EAGERs, please review NSF Proposal & Award Policies & Procedures Guide (PAPPG).

More information >>

Call for Proposals: 5th International Synthetic & Systems Biology Summer School - SSBSS 2018

The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The 2018 Summer School will take place July 25-29, 2018 at Certosa di Pontignano in Tuscany, Italy.

The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment.

Deadlines

Application: March 31, 2018

Oral Presentation/Poster Submission: March 31, 2018

Notification of Decision for Oral/Poster Presentation: April 28, 2018

Register here >>

Keynote Speakers

* PATRICK YIZHI CAI, University of Manchester, UK

* JOHN GLASS, J. Craig Venter Institute, USA

* PHILIPP HOLLIGER, MRC Laboratory of Molecular Biology, Cambridge, UK

* JENS NIELSEN, Chalmers University of Technology, Sweden

* HARRIS WANG, Columbia University, USA

* RON WEISS, MIT, USA

* LUCA ZAMMATARO, Yale University, USA

Speakers 

* Barbara Di Camillo, University of Padova, Italy

* Simone Furini, University of Siena, Italy

* Emanuele Domenico Giordano, University of Bologna, Italy

* Rodrigo Ledesma-Amaro, Imperial College London, UK

* Velia Siciliano, Italian Institute of Technology, Italy

Links

• More information on website >>
• Email via ssbss@icas.xyz
• Facebook >>

Prof Giles Oldroyd joins Sainsbury Lab to engineer nitrogen-fixing cereals

Prof Giles Oldroyd, an OpenPlant PI who directs a Bill and Melinda Gates Foundation programme of research to engineer nitrogen-fixing cereals has recently joined the Sainsbury Lab at University Cambridge after 15 years at the John Innes Centre in Norwich.

Prof. Giles Oldroyd is a leading investigator in plant-symbiotic interactions, with a particular focus on the signalling processes that allow the establishment of nitrogen-fixing and arbuscular mycorrhizal associations. His work has provided the genetic underpinnings to understand the symbiosis signalling pathway that allows rhizobial recognition in legumes and mycorrhizal associations in most plants. He explained his interests in an introductory post on the SLCU website:

"I spent 15 years working at the John Innes Centre, attempting to understand how plants perceive symbiotic microorganisms present in the rhizosphere. Having contributed to a detailed understanding of symbiosis signalling, I now want to understand how this signalling process activates the developmental changes in the root leading to the formation of a nodule and intracellular bacterial infection."

“I am very excited by the prospect that some day this research could address one of the greatest limitations to agricultural productivity”

— Prof Giles Oldroyd, SLCU

Prof Oldroyd now leads an international programme funded by the Bill and Melinda Gates Foundation and the BBSRC that is attempting to engineer cereal recognition of rhizobial bacteria as the first step towards engineering nitrogen-fixing cereals.

"There remains much to be discovered before we are likely to be able to transfer nitrogen fixation to cereals. However, I am very excited by the prospect that some day this research could address one of the greatest limitations to agricultural productivity and I am particularly motivated by the fact that the beneficiaries of my work could be some of the poorest people on the planet."

The SynBio SRI welcomes the Oldroyd Lab to Cambridge and we look forward hearing more about their work in plant synthetic biology.

Prof Giles Oldroyd's homepage at SLCU >>

Essex Synthetic Biology Summer School: 2-6 July 2018

The Essex Synthetic Biology School (ESBS) is an intensive 5-day summer course targeting students and early career scientists interested in learning cutting edge experimental and computational methods to design and build biological systems directly from world-renowned experts, working with bacterial, yeast, plant and mammalian systems, in fields such as cancer and healthcare research, as well as industrial, agricultural and environmental synthetic biology.

Synthetic biology is an emerging research and industrial field aiming at designing and engineering biological systems with specific functions. To do that, it integrates methods and technologies from biology, chemistry, engineering, computer science and mathematics to streamline the process of designing, building and testing biological systems. In the last 10 years, synthetic biology has contributed many ground breaking scientific results, including the first synthetic cell and the first synthetic chromosomes, and industrial applications, including the production of drugs and biofuels.

The School, located at the University of Essex in the U.K., comprises 20 lectures and 5 laboratory sessions, focusing on building pathways in bacteria and yeast.

Learn more and register by 1 June 2018 >>>