SynthSys-Mammalian: Edinburgh Mammalian Synthetic Biology Research Centre

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

The vision for Edinburgh's Centre for Mammalian Synthetic Biology (SynthSys-Mammalian) is to pioneer the development of the underpinning tools and technologies needed to implement engineering principles and realise the full potential of synthetic biology in mammalian systems. We have an ambitious plan to build in-house expertise in cell engineering tool generation, whole-cell modelling, computer-assisted design and construction of DNA and high-throughput phenotyping to enable synthetic biology in mammalian systems for multiple applications. In this way we will not only advance basic understanding of mammalian biology but also generate tools and technologies for near-term commercial exploitation in areas such as the pharmaceutical and drug testing industries, biosensing cell lines sensing disease biomarkers for diagnositics, novel therapeutics, production of protein based drugs e.g. antibodies and also programming stem cell development and differentiation for regenerative medicine applications. In parallel we will develop and implement new understanding of the social and economic impact of this far-reaching technology to ensure its benefits to society.

Technical Summary

Synthetic biology (SB) is defined in the UK Synthetic Biology Roadmap1 as 'the design and engineering of biologically based parts, novel devices and systems as well as the re-design of existing natural biological systems.' SB is both a platform technology and a translational technology (providing the link between a wide range of underpinning disciplines - ranging from biochemistry to systems biology - and practical applications in a wide range of different market sectors). We aim to pioneer the development of the underpinning tools and technologies needed to implement engineering principles and realise the full potential of synthetic biology in mammalian systems. We will 1. Establish a robust pipeline for the production and screening of synthetic transcription factors (sTFs) and synthetic chromatin editors (sCEs) based on the DNA binding domains of TAL effectors (TALEs) and the CRISPR/Cas system fused to transcriptional activators, repressors or chromatin modifiers e.g. histone deacetylases. 2. Create an in silico tool for designing small-molecule control of engineered protein and demonstrate the utility of this tool by producing novel drug-controlled proteins. 3. Assemble synthetic chromosomes and chromosomal safe harbors for introduction of synthetic genetic circuits. 4. Reduce contextual effects by building predictive models through characterizing circuit-chassis interactions at the single-cell level. 5.Engineer memory and computation synthetic genetic circuits in mammalian cells to a) deliver mechanistic information on the cell state, and responses to perturbations, e.g. drug treatments and count cell divisions. Underpinning this will be the development of standards for mammalian synthetic biology in collaboration with our partners NPL and take the concept of RRI in new directions to include: the politics of standardisation; the use of strategic mapping methodologies; and new approaches to engagement informed by speculative design.

Planned Impact

The SBRC focuses on building mammalian engineering capacity to benefit the life sciences, biotechnology and biomedicine.

Our deliverables for engaging with stakeholders are:

1) Through community building we will increase membership of the SBRC and double our total collaborative research income by Year 5. We will reach out locally by continuing Open Centre Meetings (fortnightly), organise monthly PI lunches preceded by a PI seminar, record seminars and both live webcast and disseminate online, hold an annual Away Day, publish a monthly newsletter, and further explore novel ways of engagement.

2) To be an internationally recognised brand with a reputation as a centre of excellence in synthetic bioengineering of mammalian systems. To do so, we will strengthen links to local networks for national phenotyping and regenerative medicine, champion the iGEM competition, continue to be active participants in three RCUK networks, link with other SBRCs and DNA Synthesis Centres, build additional international links (particularly in China, Korea, and Hong Kong), and work to host the meeting for the international synthetic yeast genome project and SynBioBeta.

3) By Year 5, we will have created an innovation environment for synthetic biology that balances the objectives and concerns of public, industry, policy, and academic communities. We will set up a Stakeholder Forum with members from industry, policy makers, regulators, and investors; maintain high visibility at Science Festivals; deepen our involvement in art-in-science events; host a writer in residence to help communicate our research; continue to make best use of the University's Press Gangs and Officers; maintain a dynamic suite of websites, have a Twitter account, and all researchers will create and promote "Research in a Nutshell" BioPodcasts; arrange 6-monthly, off-site, SynthSys Cafes to foster engagement and build dialogue; raise the profile of our activity across government through invitations to MSPs, Chief Scientists and NGOs; and maintain and grow international influence through our membership of government leadership committees. We will create a community of activity around the SBRC with at least two industrial SBRC members participating in training activities and in reciprocal secondment of staff.

A further key impact will be to generate highly skilled, responsible, and enthusiastic scientists and engineers that will move into research, management, or operational roles in private and public sectors, building the UK's capacity in synthetic biology.

We anticipate the generation of considerable intellectual property (IP) of commercial value. We will draw on Edinburgh Research and Innovation Business Development Executive, our International Advisory Board, our industrial partners, and the strength of our broader industrial network to expedite the translation of IP. We are a key partner of the Synthetic Biology Innovation Commercial and Industrial Translation Engine (SynbiCITE) and are heavily involved in both the Scottish Industrial Biotechnology Innovation Centre and the CENSIS Innovation Centre in Sensor and Imaging Systems. We will target new market sectors by developing marketing materials tailored to specific industries, holding an annual Industry Information Day to consolidate and broaden our links, and by developing an industry-engagement plan to meet industry through site visits, missions overseas and industry partnering events. By year 5, we plan three innovations in early stages of product development and to be in advanced discussion with 3-4 industry partners around R&D collaborations.

Finally, in addition to academic impacts through refereed journals and presentations at international conferences, SBRC outputs will be published in industry and policy journals, talks at national and international festivals, in media presentations, and through a portfolio of policy briefing notes that are widely distributed.

Publications

10 25 50
 
Description The UK Centre for Mammalian Synthetic Biology (the 'CMSB'), hosted by the University of Edinburgh, has had a very productive year in working towards its goals for research, training, public engagement and translation.

Our research programme is largely on schedule, although we will apply for a no-cost extension of our grant to our funders to ensure we can complete the work planned. Challenges in hiring staff have been the main cause of a delay in the research programme.

We have made excellent progress in Work Package 1 (Tools and Platform Technologies) with noteworthy success in generating libraries of synthetic transcription factors, which we are now deploying in later work packages. We are particularly excited about early evidence that cocktails of synthetic transcription factors can control stem cell differentiation as we had anticipated. These will enable us to accelerate Work Packages 3, 5 and 6 (Biotech and Medical Applications). The construction of novel genetic circuits in cells allows us to fine tune cell behaviour, of particular interest to biologics manufacturers keen to boost yield. Small molecule control of genetic circuits offers another level of sophistication for cell and tissue engineering, through drug controlled cell patterning.

Progress in our research has been evidenced by an increase in publications: over the course of 2017 we published 17 particles and have several more in a draft stage or under review.

We welcomed our second cohort of six PhD students this year. The previous year's PhD cohort benefited from bespoke training in presentation skills, team work, using social media, and working with industry. Our first Modern Apprentice completed his apprenticeship and we promoted him to Lab Technician in the Genome Foundry.

We have proactively engaged with industry, hosting visits of 13 companies new to the Centre and welcoming many repeat visits. We are exploring additional opportunities to leverage Government funding for working with industry and are exploring how to protect and exploit intellectual property arising from Work Package 1. We received an Innovate UK award for ~£1M in a joint project with Horizon Discovery and Sphere Fluidics to develop a new benchtop microfluidics system for genome and epigenome engineering.

We continue to support a variety of outreach activities including a second SAW Trust training day (reaching over 200 school pupils across Edinburgh), the Edinburgh Science Festival and University 'Doors Open' events. We have developed strategic working relationships with Science Teachers across Scotland, developing a classroom activity aimed at Scottish Higher Biology students: in this way, we can 'train the trainers' and reach more pupils. We hired an artist-in-residence to help us devise a longer-term strategy for engagement, which will encourage more sustainable engagement with the public engagement agenda.

Policy and strategy development for synthetic biology are also core to our activities: The Centre's management team are active participants in Scotland's Synthetic Biology Special Interest Group, the Industrial Biotechnology Leadership Group; the Scottish Scientific Advisory Council (SSAC), the Royal Society of Biology's Genome Editing Advisory Group; the Synthetic Biology Leadership Council.

The Centre's management team and staff continue to work hard to raise the profile of our work both in the UK and internationally. We attended >20 research and industry conferences over the year including the Mammalian Synthetic Biology workshop (Boston), Synthetic Biology: Engineering, Evolution & Design (SEED, Boston), SB7.0 (Singapore), IBioIC Annual Conference (Glasgow), SynBioBeta (London and San Francisco). We welcomed visitors from China, Japan, North and East Africa, and representatives from the US Office for Naval Research.
Exploitation Route Our first patent - of a rapid and cheap method for the production of synthetic transcription factors, the so-called STAR method - is filed and currently under licensing negotiations. One commercial collaboration (with IDT) for a multiplexing technology is under discussion.

To date we have had conversations with over 40 companies of which several have developed into potential projects. Of those, we have commercial collaborations in place with Sphere Fluidics and Horizon Discovery (Pollard), UCB (Rosser), Unilever (Rosser), Fujifilm (Rosser), Twist Bioscience (Cai/EGF). One are of interest is the application of the synthetic biology tools for bioproduction (e.g. biologics in CHO cells). We have secured a strategic relationship with Fujifilm as a partner in a new Centre for Bioprocessing 2.0 on the strength of their interest our research in mammalian synbio.

The Director has acted as an expert consultant producing reports for investment companies interested in investing in synthetic biology companies.

As well as proactively engaging with industry, we also work towards helping scope policy around how to further develop the economic potential of synthetic biology. Prof Joyce Tait is a member of a number of influential UK committees, including the Prime Minister's Council for Science and Technology and the Synthetic Biology Leadership Council (SBLC) and the centre director is a member of the SBLC science and technology sub group and we have contributed extensively to the UK synthetic biology roadmaps. On a more local level have worked closely with the Scottish Synthetic Biology Special Interest Group, to develop a framework for boosting synthetic biology business in Scotland.
Sectors Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.synbio.ed.ac.uk
 
Description The vision for the UK Centre for Mammalian Synthetic Biology (the 'Centre') at the University of Edinburgh is to pioneer the development of the essential tools and technologies needed to realize the full potential of synthetic biology for mammalian cell biology and human medicine. We remain convinced that this is a relevant, exciting and ambitious area for synthetic biological engineering and one in which we can forge a unique position. The Centre was officially launched on October 7th at a day-long event attended by over 100 delegates from academia, industry and government/NGOs. As originally envisioned, the tools of WP1 are now being deployed with success in later work packages: We are using synthetic transcription factors to control stem cell differentiation; safe harbour landing pads to modulate protein production; building Human Artificial Chromosomes to interrogate the process of cell division; and generating disease-resistant dopamine-producing cells as future treatments for Parkinson's disease. The impact of our research the course of 2018 we published 18 articles and have several more as drafts or under review. Industry continues to be interested in the potential for mammalian synthetic biology. We hosted visits from 14 companies this year and started several collaborative projects (e.g. with Synthego, UCB Pharma, Synpromics, Ingenza, Horizon Discovery). A strategic partnership (still in negotiation) with a multinational will further raise the profile of the potential of mammalian synthetic biology. Funding from our BBSRC Flexible Talent and Mobility Account has enabled us to increase the exposure of our ECRs to industry and provide industrial researchers training on our platforms. One of our ECRs is now planning a spin out company to develop a device for monitoring bioreactors. We continue to work hard to raise the profile of the Centre in the UK and internationally. We attended many academic and industry conferences over the year and are delighted to be nominated as future hosts (in 2020) of the Mammalian Synthetic Biology Workshop - the first time it has been held outside the USA. We hired Miss Jessica Fox as our artist-in-residence to help devise a longer-term strategy for public engagement. She galvanised our staff to participate in a wide variety of activities including a presentation at the Big Bang Festival (Wigtown, Dumfries), Sci-Screen talks, and she coordinated and edited a book of stories about science by our scientists. We have secured a one-year, no-cost extension to our Centre grant to November 2020, which will ensure that we can complete the research programme and deliver additional impact from our training, public engagement and industrial engagement.
Sector Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
 
Description UK Government Working Group on UK Brain Tumour Research
Geographic Reach Multiple continents/international 
Policy Influence Type Gave evidence to a government review
Impact This was far reaching review of funding, capacity building and clinical delivery of new trials and global iniativeis in brain cancer research.
 
Description ESRC-AHRC UK-Japan SSH Connections grants
Amount £32,449 (GBP)
Funding ID ES/S013601/1 
Organisation Economic and Social Research Council 
Sector Public
Country United Kingdom
Start 01/2019 
End 06/2020
 
Description Early Detection Committee - CRUK-OHSU Project Award
Amount £250,000 (GBP)
Funding ID C65925/A26986 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2019 
End 12/2021
 
Description FET
Amount € 5,000,000 (EUR)
Funding ID CyGenTiG 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 10/2018 
End 09/2023
 
Description Flexible Talent and Mobility Account
Amount £220,000 (GBP)
Funding ID BB/S508007/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 03/2021
 
Description Industrial Biotechnology Catalyst - Translation
Amount £3,200,000 (GBP)
Funding ID BB/M018229/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2015 
End 06/2020
 
Description Innovate UK Open Competition
Amount £999,381 (GBP)
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 06/2017 
End 06/2020
 
Description Keck Futures Initiatives
Amount $100,000 (USD)
Organisation W M Keck Foundation 
Sector Charity/Non Profit
Country United States
Start 06/2015 
End 06/2017
 
Description MRC Edinburgh Cellular Genomics Consortium (eCGC) pump-priming award
Amount £15,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 03/2019
 
Description Molecular control of DNA replication timing in mammalian cells
Amount € 2,000,000 (EUR)
Funding ID ERC Grant number: 726130 
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 10/2017 
End 09/2022
 
Description RAEng Chair in Emerging Technologies
Amount £1,300,000 (GBP)
Organisation Royal Academy of Engineering 
Sector Learned Society
Country United Kingdom
Start 03/2018 
End 02/2028
 
Description SynCrop: Synthetic circuits for robust orthogonal production
Amount £3,300,000 (GBP)
Funding ID 764591 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 08/2018 
End 08/2022
 
Description UCB studentship: A combined omics and synthetic biology approach to enhanced CHO cell engineering'
Amount £2,334 (GBP)
Organisation UCB Pharma 
Sector Private
Country United Kingdom
Start 10/2018 
End 09/2021
 
Description University of Edinburgh ROSSER UKRI Innovation Fellowships: BBSRC Flexible Talent Mobility Accounts
Amount £100,000 (GBP)
Funding ID BB/R506606/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 03/2019
 
Description University of Western Australia Research Collaboration Award
Amount £13,640 (GBP)
Organisation University of Western Australia 
Sector Academic/University
Country Australia
Start 01/2018 
End 12/2018
 
Title A degron controlled synthetic transcription factors have been developed 
Description The nuclease-deactivated variant of CRISPR-Cas9 proteins (dCas9) fused to heterologous transactivation domains can act as a potent guide RNA sequence-directed inducer or repressor of gene expression in mammalian cells. In such a system the long-term presence of a stable dCas9 effector can be a draw-back precluding the ability to switch rapidly between repressed and activated target gene expression states, imposing a static environment on the synthetic regulatory circuits in the cell. To address this issue we have generated a toolkit of conditionally degradable or stabilisable orthologous dCas9 or Cpf1 effector proteins, thus opening options for multidimensional control of functional activities through combinations of orthogonal, drug-tunable artificial transcription factors. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact None yet it has only recently been developed and published. 
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662744/
 
Title A prototype microbiorector device 
Description We developed an affordable prototype microbioreactor that can automate day-to-day bacterial growth and can be widely applicable. The prototype that can operate in the batch culture and turbidostat mode, is based on significantly adapting existing microbioreactor technology, making it more user-friendly and engineering it to an off-the-shelf level, while keeping the costs down. In comparisons to current bioreactors on the market, it is an order of magnitude cheaper and we envision it can replace manual flask-based culture growth. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? No  
Impact We are currently in the process of spinning out a company that will place the prototype based minimal viable product on the market. 
 
Title Cell lines - human neural stem cells and glioma stem cells 
Description Patient-derived primary cell lines from glioma tumour specimens. Also, human foetal neural stem cell lines. Plus engineered derivatives of these. 
Type Of Material Cell line 
Year Produced 2018 
Provided To Others? Yes  
Impact These cell lines provide state of the art models to explore neural stem cell biology, neural development, gliomagenesis and can be directly used in drug discovery efforts. 
 
Title Drug control of CRISPR 
Description A modification of CRISPR effectors so that they do nothing until an activating drug (tamoxifen or RU486, depending on which construct is used) is applied to cells. At that point CRISPR is activated strongly. This is both a reaerach took and has potnetial in biosafety (emergency inactivation on transgenes). 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact None yet (too recent) 
 
Title Human Artificial Chromosome 
Description Human artificial chromosome isolated from synthetic DNA construct introduced into human HT1080 cell line. Similar HACs have recently been used in screening for inhibitors of human telomere maintenance (10.1158/0008-5472.CAN-18-0894) 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact none yet 
 
Title Mouse NS cell glioma models 
Description We have exploited CRISPR/Cas genome editing and created a wealth of derivative NS cell lines that will serve as important and useful models of the human disease. These include a set of glioma cell lines that are now being validated. 
Type Of Material Cell line 
Year Produced 2016 
Provided To Others? Yes  
Impact These cell lines are being used by CRUK Career Development Award holder Dr Dirk Sieger to explore glioma and microglia interactions using the zebrafish as a model system. 
 
Title Optogenetic control of cell death 
Description Cells can be saved from drug-inducible cell death by an optogenetic construct 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact It has been one of the foundations of a 5 million Euro collaborative project (CyGenTiG), in which light will be used to control morphogenesis. 
 
Title Plasmids for production of TAL effectors 
Description Library of plasmid parts for creation of synthetic transcription factors based on TAL effector architectures. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact Publication of method was carried out. Various laboratories are accessing the plasmids. 
URL https://www.addgene.org/kits/pollard-star-tale-assembly/
 
Title non-invasive tool to control subnuclear localisation of specific loci 
Description By taking advantage of Cas9/CRISPR technology, we have designed a method to control sub-nuclear localisation of any genomic locus without altering its genetic or epigenetic composition. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? No  
Impact This method will allow to manipulate nuclear architecture without affecting primary DNA sequence. This is a fundamental tool to understand the role of nuclear architecture during gene expression control. 
 
Title two-step locus-specific targeting of big cargos 
Description Locus-specific insertion of big DNA cargos in the mammalian genome, without using selection markers, as never been achieved. Absence of an expressed drug-resistance or fluorescent marker is very important when the locus is heterochromatic and silent. Expression of the selection in this cases is either unsuccessful or induces changes of the chromatin state of the locus. We have devised a two step system to achieve successful targeting of these type of loci. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? No  
Impact Our method allows controlling subnuclear localisaiton or protein tethering of heterochromatin loci without perturbing their epigenetic makeup. 
 
Title synPHARM 
Description SynPharm is a database of ligand-responsive protein sequences, derived from interactions from the Guide to PHARMACOLOGY and using data from the Protein Data Bank. The sequences here are obtained by identifying the protein chain that interacts with a ligand for a given Guide to PHARMACOLOGY interaction, determining the binding residues, and producing a continuous 'bind sequence' that can be used to confer drugability to another protein. Each bind sequence also contains metrics such as atomic contact ratio and proportional length, and visualisations such as the residue distance matrix, to allow you to better judge whether a sequence is likely to be able to fold independently. The rationale for such a project was to enable the development of orthogonal molecular switches - switches which only respond to an exogenous molecular trigger, which itself will not interfere with endogenous receptors. 
Type Of Material Data analysis technique 
Year Produced 2016 
Provided To Others? Yes  
Impact Text written March 2017: We have used the tool to generate druggable versions of Cas9 and cpf1 for inducible gene editing (paper in preparation). The database was put on full public release so recently that we are not yet aware of external impacts, but we have just added a Google Analytics counter to track external use. 
URL http://synpharm.guidetopharmacology.org/
 
Description Collaboration in the design and use of human artificial chromosomes 
Organisation National Cancer Institute (NCI)
Country United States 
Sector Public 
PI Contribution We have isolated plasmids that have been used to create new two-domain human artificial chromosomes.
Collaborator Contribution They constructed one of the plasmids used in this construction. They also provided facilities where Elisa Pesenti learned how to analyse these plasmids. Lastly, they performed Southern Blot Analysis of several of the human Artificial Chromosomes that we isolated.
Impact There have been many outputs from this collaboration. The two relevant to the present grant are shown in my research portfolio.
 
Description Collaboration with Dr Elise Cachat 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Elise Cachat was the post-doc on this grant, but partly on the strength of what she achieved she now has an independent position and we now collaborate as equals.
Collaborator Contribution Experimental design and computer modelling.
Impact Publication: Cachat E, Liu W, Davies JA (2017) Synthetic self-patterning and morphogenesis in mammalian cells: a proof-of-concept step towards synthetic tissue development. Eng Biol 1: doi: 10.1049/enb.2017.0013
Start Year 2016
 
Description Foundry becomes the first academic member of the International Gene Synthesis Consortium (IGSC) 
Organisation International Gene Synthesis Consortium
Country United States 
Sector Charity/Non Profit 
PI Contribution The University of Edinburgh's Genome Foundry has become the first academic member of the International Gene Synthesis Consortium (IGSC), an association of the world's leading gene synthesis companies working to safeguard the rapidly-emerging field of gene synthesis. The IGSC was founded in 2009 by the world's leading gene synthesis companies to advance biosecurity across the industry. In April 2015, the IGSC became a California not-for-profit 501(c)(3) corporation under charter and by laws developed to facilitate broader membership and community participation. The IGSC's goals are (a) to educate gene synthesis companies and the public regarding sequence and customer screening of synthetic gene orders; (b) to identify and prevent the unauthorized synthesis and sale of inappropriate sequences; and (c) to coordinate development of ongoing best practices. For more information about membership or the IGSC screening process, please visit www.genesynthesisconsortium.org.
Collaborator Contribution The IGSC was founded in 2009 by the world's leading gene synthesis companies to advance biosecurity across the industry. In April 2015, the IGSC became a California not-for-profit 501(c)(3) corporation under charter and by laws developed to facilitate broader membership and community participation. The IGSC's goals are (a) to educate gene synthesis companies and the public regarding sequence and customer screening of synthetic gene orders; (b) to identify and prevent the unauthorized synthesis and sale of inappropriate sequences; and (c) to coordinate development of on going best practices. For more information about membership or the IGSC screening process, please visit www.genesynthesisconsortium.org.
Impact This collaboration requires that all parties adhere to the gene screening guidelines to ensure biosecurity.
Start Year 2016
 
Description Integrated DNA Technologies 
Organisation Integrated DNA Technologies
Country United States 
Sector Private 
PI Contribution We worked with IDT to test via early access their reagents for CRISPR genome editing to knock-in epitope tags.
Collaborator Contribution The partners provided £10K worth of reagents for testing. These were synthetic RNAs and long DNA oligonucleotide repair templates.
Impact We have created a large panel of mouse and human engineered neural and glioma stem cell lines with knockin reporters. These are used as research tools.
Start Year 2017
 
Description Janssen Pharmaceuticals 
Organisation Johnson & Johnson
Department Janssen Pharmaceuticals
Country United States 
Sector Private 
PI Contribution We have collaborated with Janssen in a drug screening project as part of the National Phenotypic Screening Centre - Phenomoics discovery initiative (PDi). We have performed a small molecule screen in search of compounds that affect glioblastoma stem cell self-renewal, making use of an engineer Sox2 knockin reporter line.
Collaborator Contribution Janssen has provided libraries of their small molecules, chemiinformatics support, access to the tool compounds for validation.
Impact Outputs are new hits to support future anticancer drug discovery efforts against glioblastoma.
Start Year 2017
 
Description Molecular Dynamic modelling of nucleosome interarctions with Transcription factors 
Organisation Royal Netherlands Academy of Arts and Sciences
Department Hubrecht Institute
Country Netherlands 
Sector Academic/University 
PI Contribution By generating various mutants forms of transcription factors and measuring the biochemical affinity to nucleosomes in vitro and to chromatin in cells, we have identified important regions for nucleosome binding.
Collaborator Contribution Using Molecular dynamics modelling, our collaborators used our experimental data to model the three dimensional structure of transcription factors in complex with nucleosomes.
Impact Organized joint meeting. manuscript under preparation.
Start Year 2017
 
Description Ramified Rolling Circle Amplification for nucleosomal DNA synthesis 
Organisation Utrecht University
Country Netherlands 
Sector Academic/University 
PI Contribution We have used DNA synthesized by our collaborators to reconstitute nucleosomes in vitro
Collaborator Contribution To enable studies on native, genomic nucleosomes, our collaborators establshed an efficient and flexible method to produce nucleosomal DNA based on rolling circle amplification (RCA).
Impact manuscript under revision
Start Year 2017
 
Description Reprogramming pancreatic cancer (PDAC) to discover early markers 
Organisation Oregon Health and Science University
Country United States 
Sector Academic/University 
PI Contribution We aim to profile the chromatin landscape of PDAC during reprogramming to iPSCs using ATAC-seq and ChIP-seq for histone marks. Characterizing these chromatin-barriers would be particularly important as we reason it will reveal the essential epigenetic transition from the PanIN to PDAC stages.
Collaborator Contribution Our collaborator will reprogram a large number of PDAC tissue from human patients to iPSC to model cancer progression in mice.
Impact CRUK-OHSU project award
Start Year 2019
 
Description Transcription factors lineage specificity during reprogramming 
Organisation Hebrew University of Jerusalem
Department Hebrew University Hadassah Medical School
Country Israel 
Sector Academic/University 
PI Contribution We are using wide variety of genomic approaches including ChIP-seq, RNA-seq, Mnase-seq and ATAC-seq combined with bioinformatics to define how various combinations of transcription factors engage the genome and establish specific cell identity during reprogramming adult cells to embryonic stem cells and trophoblast cells
Collaborator Contribution Our collaborators have developed various methods of reprogramming to trophoblasts and embryonic stem cells and have carried out RNA-seq and ATAC-seq at different stages of reprogramming.
Impact Manuscript under preparation. two grants submitted
Start Year 2016
 
Description Twist bioscience 
Organisation Twist Bioscience
Country United States 
Sector Private 
PI Contribution Testing of double stranded DNA blocks synthesised for targeting vector production.
Collaborator Contribution Provision of double stranded DNA blocks synthesised for targeting vector production.
Impact Production of novel engineered cell lines.
Start Year 2018
 
Title BandWitch 
Description BandWitch is fragment analysis framework. Given a batch of assemblies, BandWitch will suggest the best enzymatic digestion to create easily-interpretable patterns for all constructs. Then, when the constructs have been experimentally digested and migrated, BandWitch provides methods to validated the batch and generate informative reports indicating which constructs are structurally correct, and helping to troubleshoot constructs with invalid band patterns. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact BandWitch is used routinely at the Edinburgh Genome Foundry where it significantly accelerated the construct validation work-flow. One manuscript for publication in preparation. 
URL https://github.com/Edinburgh-Genome-Foundry/BandWitch
 
Title Caravagene 
Description Simple library to plot and highlight DNA design 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This library is routinely used at the Edinburgh Genome Foundry to communicate designs to customers in the setup stage of custom assembly projects 
URL https://github.com/Edinburgh-Genome-Foundry/Caravagene
 
Title Cell counter 
Description The software automatically counts numbers of cells in a given sequence of images. 
Type Of Technology Software 
Year Produced 2018 
Impact The software will likely be a part of a spin-out company and a device in development. We are currently looking into protecting it. 
 
Title DNA Chisel 
Description A flexible, extensible Python library to optimize nucleotide sequences with respect to constraints and objectives. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Used routinely at the Foundry to help customers shape their projects (go from human-formulated specifications to an actual DNA nucleotides sequence) and save time and money by maximizing the chances of assembly success. One publication in preparation. 
URL https://github.com/Edinburgh-Genome-Foundry/DnaChisel
 
Title EMMA-DB (now DAB) 
Description In-progress web application for Computer-Aided-Design of genetic constructs, with integrated ordering to the Edinburgh Genome Foundry. The application allows to manage genetic parts for different leading assembly standards (MoClo, EMMA, etc.), to browse the parts repository of the EGF and other users, and to design constructs from these parts, and to send the order to the EGF. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact The software will serve as a customer front-end for the foundry, allowing for the planning and manufacturing of customer orders with minimal human intervention. As of February 2018 it is released in an alpha version for tests by a restricted group of customers. It supports mostly the EMMA assembly standard, and is being extended to support other standards and reach a bigger community. The software also proposes some novel approaches to construct design and may be the subject of a publication later on in 2018. 
URL https://dab.genomefoundry.org/
 
Title Edinburgh Genome Foundry File Management System 
Description Server and network configuration allowing to transfer files from or to different computers of the Edinburgh Genome Foundry (and in particular robot computers) in a friendly, safe, and traceable way. 
Type Of Technology Software 
Year Produced 2017 
Impact The EGF file management system strengthens the EGF operations in several ways. (1) By allowing files to be easily moved from an operator's computer to a robot's computer, it decreases the time necessary to set up robotic operations and reduces the risk of human error by file confusion. (2) By backing up all the managed files, the file manager ensures that no information is lost. (3) By keeping a trace of files histories, the file manager enables to recover information about past robotic runs, thus ensuring good traceability and making troubleshooting of operations easier - we can know at any time what exact protocol was ran on each robot at any given date. 
 
Title Edinburgh Genome Foundry Website 
Description Customer front of the Edinburgh Genome Foundry, with informations on the Foundry's services, products, software efforts, team, and contact details. the website also features an interactive strain ordering application. 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact The website if one of the main elements of the Edinburgh Genome Foundry's online presence strategy, allowing the Foundry to market its activity globally. The development of the website has also established a visual identity of the Foundry. 
 
Title Fitderiv 
Description The software is written to provide a tool for estimating growth rates from optical density data and uses that language (although it can process any other type of data too). It has been described in more detail in the following publication Swain P S**, Stevenson K, Leary A, Montano-Gutierrez L F, Clark I B N, Vogel J and Pilizota T. Inferring time-derivatives, including cell growth rates, using Gaussian processes. Nature Communications 2016;7:13766 and made openly available at http://swainlab.bio.ed.ac.uk/software/fitderiv/ 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The software is currently used by several research groups and expected to be adopted wider (publication date is December 2016) 
URL http://swainlab.bio.ed.ac.uk/software/fitderiv/
 
Title Genedom 
Description Genedom is a python library for managing the domestication of genetic parts (i.e. the modification of their sequence so as to make them compatible with a given genetic assembly standard). Genedom binds together a sequence optimizer, genetic standards informations, and a reporting routines, to automate the domestication of large batches in an easy and human-friendly way. 
Type Of Technology Software 
Year Produced 2018 
Impact Genedom can do in a minute a task which would take a human operator a full day, and avoids human mistakes which can be very costly at this step. It has been used to quickly domesticate and order hundreds of parts for Edinburgh Genome Foundry cuistomers. 
URL https://edinburgh-genome-foundry.github.io/genedom/
 
Title Golden Hinges 
Description A library to find collections of compatible overhangs for Type-2S restriction-based assembly. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The early version of the library was used to help in the design of the overhangs of the EMMA standard, which is now a main product of the EGF. The library has been further used to compute overhangs for 4+ custom design projects at the Foundry. 
URL https://github.com/Edinburgh-Genome-Foundry/GoldenHinges
 
Title Icebreaker 
Description Python library to communicate with the JBEI-ICE DNA sequence manager. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact This library is now a central piece of software in the Edinburgh Genome Foundry as it provides our internal web applications with the informations (DNA sequence and sample availability) from our sequence manager. It saves hours of work to human operators weekly by automatically processing the upload or download of hundreds of DNA parts sequences. 
URL https://edinburgh-genome-foundry.github.io/icebreaker
 
Title Kappagate 
Description Experimental computational software to predict the difficulty of a DNA assembly using Golden-Gate like standards: given a set of parts to assemble, Kappagate will run a simulation to predict which proportion of the final clones will contain the right version of the DNA assembly. From this prediction, Kappagate can inform the experimentalist of how many clones they should pick 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Knowing how difficult a construct will be to assemble is important for a Foundry for deciding whether the order is worth taking in. Knowing how many colonies should be picked to obtain a valid clone is important for predicting costs (Quality Control is a significant part of the final assembly cost). 
URL https://github.com/Edinburgh-Genome-Foundry/kappagate
 
Title Primavera 
Description Primavera is a framework for primer-based DNA assembly verification (Sanger sequencing and PCR validation). Given a batch of assemblies, Primavera can generate an optimal set of primers to verify the constructs, leveraging on already-available primers. Primavera can also be used to create easy-to-read validation reports from Sanger sequencing data. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Primavera is used at the Edinburgh Genome Foundry to automate the planning of sequencing batches for assembly verification. 
URL https://github.com/Edinburgh-Genome-Foundry/Primavera
 
Title Saboteurs 
Description Saboteurs is a Python library (and associated web app) to detect failure-causing elements from success/failure data. In particular it can use logical and statistical methods to identify genetic parts associated with assembly failure. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Saboteurs is used systematically every time a batch of assembly has a high failure rate in the Edinburgh Genome Foundry. It has succesfully saved hours of troubleshooting by identifying parts whose samples were indeed corrupted. 
URL https://edinburgh-genome-foundry.github.io/saboteurs
 
Title Screepy 
Description Pathogenicity screening framework implementing the protocol of the International Gene Synthesis Consortium (BLAST search against databases of blacklisted agents) 
Type Of Technology Software 
Year Produced 2017 
Impact As a member of the International Gene Synthesis Consortium, the Edinburgh Genome Foundry screens DNA orders to ensure that they are safe. Pathogenicity screening is a non-trivial task with "grey areas" as the (non-)pathogenicity of a sequence is not always obvious. The Screepy framework produces comprehensive reports providing the Foundry operators with the relevant results to take an informed decision. 
 
Title Sequenticon 
Description Python library (and associated web app in CUBA) to generate human-friendly icons representing sequences in an unambigous way: if two sequences have the same icon, they are certainly the same sequence. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Sequenticons are used mostly in PDF reports to increase traceability in the foundry: if a customer suddenly changes a part's sequence without modifying its name, this can cause serious confusion. Using sequenticons makes it possible to understand at a glance whether two parts in two different reports are actually the same part or not. 
URL https://github.com/Edinburgh-Genome-Foundry/sequenticon
 
Title Smart Assembly 
Description Collection of web applications for the internal operations of a DNA assembly Foundry. Leveraging on the computational software of the Edinburgh Genome Foundry, Smart provides user interfaces for order processing (validation of the order, cloning simulation, automatic enzyme selection, robotic files generation) and sample management (creating/moving/updating microplates in the sample manager, or batch-uploading new parts to the foundry's repository) 
Type Of Technology Software 
Year Produced 2017 
Impact Smart Assembly is a central software tool of the Edinburgh Genome Foundry where it integrates together the computational software and databases of the Edinburgh Genome Foundry, allowing for the planning of assembly batches (from order validation to picklist generation), and high-level sample management (creating/moving/updating plates). 
 
Title SynPharm software tools 
Description Tools for assisting the design of druggable proteins 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This is a foundation for the Synpharm database 
 
Title Topkappy 
Description Simple Python API for the Kappa simulation framework. Topkappy enables to represent chemical agents (e.g. DNA fragments) and interactions (e.g. ligation) in a programmatic way, making it possible to define and simulate complex problems with hundreds of agents and interactions. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Originally developped to support the development of Kappagate (framework for assembly difficulty prediction, also listed in the same Awards), Topkappy was eventually packaged as a project of its own as it can be useful to the community. 
URL https://github.com/Edinburgh-Genome-Foundry/topkappy
 
Title Visual SBOL CSS 
Description Simple library to display genetic designs using the SBOL Visual language 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Used routinely to display genetic constructs in the internal software applications of the Edinburgh Genome Foundry. 
URL https://github.com/Edinburgh-Genome-Foundry/SBOL-Visual-CSS
 
Title Zymp 
Description Small Python library (and associated web app on CUBA) to design sequences with compact arrays of restriction sites. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact Used originally to develop custom control sequences for manufacturing and quality control at the foundry, it has been packaged in the hope that it will be useful to the community. 
URL https://github.com/Edinburgh-Genome-Foundry/zymp
 
Title blabel 
Description Blabel is a python library to programmaticaly generate labels (typically for printing stickers) with barcodes and other dsplays 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Blabel is used to print microplate barcodes and other custom labels at the Edinburgh Genome Foundry, with the day's date, correct genetic part names (via interfacing with our sequences manager) etc. 
URL https://edinburgh-genome-foundry.github.io/blabel
 
Title python_codon_tables 
Description Small Python library providing codon optimization tables for virtually any species, either via built-in data tables, or by automatically downloading the table corresponding to a given TaxID from the internet (http://www.kazusa.or.jp) 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Since 2019 this library provides codon tables data to all applications of the Edinburgh Genome Foundry which perform codon optimization (DNA Chisel, Genedom, and projects using these). 
URL https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables
 
Description BBC Arabic TV Visit 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Visit from Anees Al Qudaihi, from BBC Arabic World Service, who was making a future edition of a Science and Technology programme.
Year(s) Of Engagement Activity 2016
 
Description Biological Art Public Lecture Summerhall 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Biological artists Oron Catts and Ionat Zurr presented their on-going work in collaboration with Centre researchers in an event chaired by Jane Calvert.
Year(s) Of Engagement Activity 2018
URL http://www.ascus.org.uk/contextualising-biotechnological-artifacts/
 
Description Cafe Synthetique - Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact On 9th of October, researchers from Biology, Informatics and Engineering hosted Edinburgh's first Café Synthetique event. This monthly event aims to address the lack of public and informal events for those curious about Synthetic Biology. Monthly meetings are held with two short talks and then dialogue over pizza.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/edinburghs-first-cafe-synthetique
 
Description Closing the Loop Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In little over a decade, synthetic biology has evolved from demonstrating proof-of-concept gene circuits in bacteria to developing a new class of therapeutic devices (theranostics). However, despite a thriving community, and some noteworthy successes, the task of assembling a predictable gene network from biomolecular parts remains a challenge. It can take many months of trial and error to produce a gene circuit with the desired behavior or phenotype. In engineering terms, we are still far from the efficient, rational 'Design-Build-Test' cycle deployed in industrial manufacturing contexts.

To gain consensus about the challenges, and to discuss potential solutions, the UK Centre for Mammalian Synthetic Biology hosted a workshop on February 22nd and 23rd 2018 in Edinburgh. A principal aim of the workshop, besides knowledge exchange across the different communities, was to start to develop a roadmap document and a focused community to address these challenges through targeted funding applications.

Over 50 people from US, UK and Europe attended the workshop and enjoyed two days of talks and lively discussion. They discussed four key areas:
•How to automatically design synthetic gene circuits - Bio-design automation;
•How to design the most informative experiments to characterize such circuits - Optimal Experimental Design;
•How to use such experiments to obtain reliable mathematical models - Making sense of data;
•What kind of technologies those experiments should be based on - Technology.

Outputs of the meeting will be used to develop a community position paper.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/international-workshop-discuss-unmet-needs-%E2%80%98design-build-t...
 
Description Crossing Kingdoms Exhibition at Edinburgh International Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Edinburgh International Science Festival hosted an arts exhibit by biological artists Oron Catts and Ionat on 'Crossing Kingdoms', their collaborative work with the Centre from 31st March - 13th May 2018 at Summerhall, Edinburgh.
Year(s) Of Engagement Activity 2018
URL https://www.summerhall.co.uk/visual-arts/pig-wings-crossing-kingdoms/
 
Description Doors Open Day 2017 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact This year, Doors Open was even bigger and better than last as we welcomed over 200 visitors to the Roger Land Building - home to the Centre - on Saturday 23rd September to find out more about the great science we do within its walls. As part of the national Door's Open weekend, Centre staff and Edinburgh undergraduate iGEM team, came along to engage the public with some of the great projects ongoing across the Centre and School of Biological Sciences. Children had an opportunity to engineer their own fuzzy felt engineered bacteria, watch how bacteria can clean up dirty water, and how robots can take the pain out of pipetting! We were particularly delighted to welcome members of the Colouring Outside the Lines group of autistic girls interested in STEM subjects. They came for a private viewing before the opening to the general public and asked some very challenging questions.
Year(s) Of Engagement Activity 2017
URL http://www.synthsys.ed.ac.uk/news/synthetic-biology-opens-doors
 
Description Edinburgh Doors Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact This year, the Centre welcomed 367 visitors to the Roger Land Building on Saturday 29th September where they explored science as varied as synthetic biology through to infectious diseases.

The Centre provided hands on arts and crafts activity, designed by Dr Gaynor Campbell, to explain how we can engineer in novel features to cells to make them useful tools to fight major global challenges. Kids also got involved with designing and building plasmids to encode their features of choice - from oil munching bacteria to new enamel for teeth.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/doors-open-day-attracts-more-visitors
 
Description Edinburgh Doors Open Day 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact On September 26th, SynthSys opened the Waddington Building to the public for the first time during the Doors Open event. Over the course of the day we had 75 visitors come to explore about our multidisciplinary research that brings biology together with engineering. We had exhibits from the lab of Dr Timm Krueger who offered hands-on interactive on a novel method for sorting cells, useful potentially in medicine. The lab of Prof Chris French explained how cells can be engineered to detect arsenic in drinking water, a project that may help the 100 million people at risk in developing countries. Members from the lab of Dr Patrick Cai offered a fun demonstration of the value of high-throughput and automated technology for printing cells (see photos). Dr Louise Horsfall's lab treated guests to the wonders of fluorescent bacteria and how bugs can be designed to clean up contaminated soil. Finally, visitors could actually check for themselves how climate change impacts on plant growth by playing with parameters of a model generated in the lab of Professor Andrew Millar. Edinburgh Doors Open Day is organised by the Cockburn Association (Edinburgh's Civic Trust). Now in its 25th year, the event has become one of the capital's most popular free days out. For the day Edinburgh's most architecturally, culturally and socially significant buildings are opened to the public. Many of our visitors asked probing questions about our research and several were potential undergraduate students considering training in synthetic biology.
Year(s) Of Engagement Activity 2015
URL http://www.synthsys.ed.ac.uk/news/opening-doors-synthsys
 
Description Edinburgh Doors Open Day 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Over 70 visitors enjoyed learning about synthetic biology and its many applications at the Edinburgh Doors Open event in the Roger Land Building on Saturday 24th at the King's Buildings Campus. Staff and postgraduate students from SynthSys, and this year's Edinburgh iGEM team, came along to explain more about their research and the power of synthetic biology. They were joined by staff from the Centre for Regenerative Medicine, who explained how stem cells are being used to create cells suited for therapy. Children had an opportunity to engineer their own fuzzy felt bugs, parents contemplated stem cells under a microscope and visitors were amazed at the metal munching power of microbes. Many of our visitors were quite unaware of the work we do and its potential impact for society. There were many animated conversations from both adults and children about synthetic biology.
Year(s) Of Engagement Activity 2016
URL http://www.synthsys.ed.ac.uk/news/open-doors-synthetic-biology
 
Description Edinburgh International Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The Centre took synthetic biology to the Edinburgh Science Festival from March 31st to April 4th. Part of the School of Biological Science's 'Biodiscoveries' activities, the Centre sought to explain the fundamentals of synthetic biology to the primary school age visitors and their carers and to showcase some of the exciting research projects underway in Edinburgh. Over 2,500 attended the event, with lots of questions and interactions from the young visitors.
Year(s) Of Engagement Activity 2016
URL http://www.synthsys.ed.ac.uk/news/fuzzy-felt-festival-science
 
Description Exhibit at a Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Centre members braved the erratic Edinburgh summer weather to build bugs with kids of all ages at the annual Meadows Festival. Over 100 children came along during the event to design and build bugs with super powers that could help to save the planet.

The activity, designed by Dr Gaynor Campbell, explains very simply how we can engineer in novel properties to cells to make them useful tools in the fight to address many global challenges. Participating kids totally got with the programme and built some fantastic creations - and all in a friendly GM-free environment. It also provided an opportunity to explain the Centre's research to parents and carers.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/building-superbugs-meadows
 
Description Exhibitor at 2016 Industrial Biotechnology Showcase 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Centre showcased its research activities and industry partnerships to over 400 delegates attending the annual conference of the Industrial Biotechnology Innovation Centre (IBioIC) in Glasgow on January 28th and 29th. We had a stand within the exhibition hall displaying pop-up banner and marketing materials. Professor Susan Rosser, Director of the Centre for Mammalian Synthetic Biology, chaired a session on the challenges and opportunities arising from synthetic biology. The meeting generated many new leads with key industry players and other potential academic collaborators.
Year(s) Of Engagement Activity 2016
URL http://www.synthsys.ed.ac.uk/news/synthsys-exhibits-annual-industrial-biotechnology-innovation-centr...
 
Description Exhibitor at IBioIC Annual Conference Jan 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact The Centre sponsored an exhibition stand at the third Annual Conference of the Industrial Biotech Innovation Centre (IBioIC), which attracted over 400 delegates over two days in late January.
Year(s) Of Engagement Activity 2017
URL http://www.synthsys.ed.ac.uk/news/delivering-impact-industrial-biotech-conference-2017
 
Description Exhibitor at IBioIC Annual Conference Jan 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Sponsored a session on synthetic biology at the 2018 Fourth Annual Conference of the Industrial Biotechnology Innovation Centre. Prof Joyce Tait chaired the sponsored session on synthetic biology spin outs. The exhibit and sponsorship helps to raise the profile of the synthetic biology research ongoing in Edinburgh; our continued visibility is key to driving new connections and collaborations with industry.
Year(s) Of Engagement Activity 2018
 
Description Exhibitor at KTN Chemistry and Industrial Biotechnology (IB) Showcase in York 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact The Centre attended the KTN Chemistry and Industrial Biotechnology (IB) Showcase in York on Sept 20 and 21 representing the Synthetic Biology Research Centres and Facilities across the UK, which now amounts to ~£300 million UK Government investment. The Centre Director chaired a session on Synthetic Biology during the event.
Year(s) Of Engagement Activity 2017
URL http://www.synthsys.ed.ac.uk/news/full-speed-ahead-uk-bioeconomy
 
Description Exhibitor at SynBioBeta London 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact The Centre had a stand at SynBioBeta in London April 2016 alongside our other sister BBSRC funded SynBio Research Centres. Several hundred delegates attended from the UK and overseas. The meeting enabled us to network with other colleagues from across the UK and beyond, network with industry executives and investors and also better understand the commercial synbio landscape.
Year(s) Of Engagement Activity 2016
URL http://www.synthsys.ed.ac.uk/news/synbioblog-synbiobeta-london-2016
 
Description Formal Launch of the UK Centre for Mammalian Synthetic Biology 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Centre was officially launched on October 7th at a day-long event attended by over 100 delegates from academia, industry and government/NGOs. There was an overview of the vision of the centre and some of the key work packages. One of our Board members provided a keynote talk and discussion by industry. During the event we also hosted first SynBioBeta Activate event in Scotland with over 80 attendees.
Year(s) Of Engagement Activity 2015
URL http://www.synthsys.ed.ac.uk/news/uk-centre-mammalian-synthetic-biology-launched
 
Description Foundry official launch event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact To celebrate the EGF opening, the University hosted a second SynBioBeta Activate! event in Scotland in partnership with Scottish Enterprise. This event attracted nearly 200 delegates and delivered a lively afternoon of discussion and debate on the role of automation and robotics in synthetic biology. There was a lineup of distinguished international speakers with an inspiring keynote from Ye Yin, CEO of BGI who talked about their ambitious plans in synthetic biology. Delegates then enjoyed short presentations from some of the leaders in DNA design and assembly automation including Cambridge Consultants, Labcyte, Thermo Scientific, Pacific Biosciences, Autodesk, m2p Labs.
Year(s) Of Engagement Activity 2016
URL http://www.synthsys.ed.ac.uk/news/edinburgh-map-dna-design-and-construction
 
Description Hosted visits to the Edinburgh Genome Foundry by diverse groups. These included scientists, politicians, undegraduate and prospective students, as well as representatives of industrial companies and funding agencies. 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Visitors to the facility had a brief introduction to the aims of the work and technology involved in the Edinburgh Genome Foundry. This was typically followed by a visit to see the state-of-the-art in operation. Visitors were always stimulated to ask further questions about the operation of the facility and the wider goals of synthetic biology. 2-3 tours were conducted per week throughout the year.
Year(s) Of Engagement Activity 2016,2017,2018
 
Description International Workshop - Future Trends in Synthetic Biology 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A group of 50 leading synthetic biologists gathered at the Edinburgh Centre for Carbon Innovation in Edinburgh on May 16 and 17 to discuss 'Future Trends in Synthetic Biology.'

Hosted by the UK Centre for Mammalian Synthetic Biology the purpose of the 2-day workshop was to discuss and report on current research progress in the field of synthetic biology, and discern focal points for future, related disruptive technologies and applications. The workshop was an invitation-only, closed-door event to provide an opportunity for participants to discuss their perspective without bias.

During the event there was animated discussion around a range of topics, from the application of synthetic biology to accelerate the production of high value chemicals, materials and medicines, through to heated debate on issues such as proportionate governance, biosecurity and ethics. At the end, delegates discussed what measures might be needed to help move synthetic biology to the next levels. Issues such as universal standards, identify 'grand challenges' focusing the community on a shared goal, and coordinating all relevant stakeholders were discussed.

A white paper discussing the discussion of the meeting and its recommendation will be shared with the community when completed.

The Centre would like to thanks the US Office of Naval Research Global and the Department of Homeland Security for sponsoring this event and in particular to Dr Patrick Rose (ONR Global) for all his support with its organisation and delivery.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/centre-hosts-future-trends-workshop
 
Description Laboratory Tours for Children with Cancer, Cancer Research UK and The Brain Tumour Charity 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact Laboratory tour of facilities and discussion about brain cancer and progress being made.
Year(s) Of Engagement Activity 2015,2016,2017,2018
 
Description MSP visit to Foundry 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Visit from local MSPs Ian Murray and Daniel Johnson
Year(s) Of Engagement Activity 2016
 
Description Midlothan Science Festival - Exhibit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Alazne Dominguez came up with a clever, hands-on approach for building a dialogue around synthetic and systems biology. They engaged with 94 kids (aged 5 to 11) with the concepts of synthetic biology and bioinformatics through an activity titled: Decoding and Designing. Why? They wanted to show the simplicity of these apparently complicated concepts in a fun and educative way through interactive activities.

We attended two events within the festival: First, the 'Science Alive Gala Day' at Lasswade High School, Bonnyrigg and then the 'Computer Festival' at IKEA, Straiton.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/decoding-and-designing-out-and-about-midlothian-science-festival
 
Description Midlothian Science Festival 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We took our 'Master Biobuilder' to he Midlothian Science Festival over a weekend in October. This enables us to reach out to less advantaged regions around Edinburgh and share our interest in Synthetic Biology. There was good engagement as this event from visitors.
Year(s) Of Engagement Activity 2016
 
Description Participation in AGM at Uganda Virus Research Institute 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact On February 8-10, Prof Susan Rosser, Prof Alistair Elfick and Dr Liz Fletcher attended the AGM of the MUII-Plus DELTAS programme held in Entebbe, Uganda, at the Uganda Virus Research Institute.

The MUII-Plus programme is well established and is directed largely to exploring the aetiology and pathology of infectious diseases pertinent to Sub Saharan Africa. The research initiative is funded by the Wellcome Trust, UK Aid and NEPAD and its long-term vision is to train African leaders in bioinformatics, immunity and infectious diseases, which it is doing admirably well.

Over three days, the Edinburgh team got a great insight of endemic diseases such as parasitic infections (Schistosomiasis, Trypanosomiasis), tuberculosis and HIV, which continue to be the source of major sources of ill health in Uganda and Sub-Saharan Africa (SSA) more widely. An analysis of the ongoing research and areas of unmet needs will follow.

On the first day of the event, the Centre team presented to >50 delegates on what synthetic biology was and the many opportunities to deploy it towards research challenges for infection and immunity. This was certainly a new area of research to most individuals in the room, many of them quite taken (if not amazed!) at the potential opportunities arising. Several discussions have arisen about applications for synthetic biology, including potential collaborative projects with UK-based researchers who had also attended the event.

We later ran a workshop, facilitated by Alison Gray (Skillfluence) on 'Creative Problem Solving' bringing together 25 senior managers and researchers from the University of Makerere and local hospital for a brainstorm.
Year(s) Of Engagement Activity 2017
URL http://www.synthsys.ed.ac.uk/news/exploring-grand-challenges-uganda
 
Description Participation in Big Bang Science Weekend in Wigtown 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Big Bang Weekend is an annual event that explores different aspects of science for the public. This year the topic was 'Is it alive?' which explored what we mean by life at both large and small scales. There were great presentations on robots and artificial intelligence, whether or not there is life out there in space, and a comedian's exploration of human consciousness (or lack thereof).
There were a series of talks for the general public. Around 80 people attended the presentation.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/should-vegans-eat-yeast
 
Description Participation in Royal Society of Biology careers event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Workshops on careers for biology graduates, held at the University of Highlands and Islands, and attended mainly by professional careers advisors, with some undergraduate attendance too. It was intended for the careers advisors.
Year(s) Of Engagement Activity 2017
 
Description Presentation of the Edinburgh Genome Foundry and uses of synthetic biology at a University Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Edinburgh Genome Foundry (EGF) staff presented a poster and some hands on material to explain to interested members of the general public, what the work in the EGF involves, why automation of processes is especially important in the field of synthetic biology and how synthetic biology will be of great importance for the future.
Year(s) Of Engagement Activity 2017
 
Description Sci-Art Collaboration and Exhibit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact For two weeks in January 2018, SynthSys and Science Technology and Innovation Studies (STIS) jointly hosted pioneering biological artists Ionat Zurr, Oron Catts and Tarsh Bates from SymbioticA: the Centre of Excellence in Biological Arts at the University of Western Australia.

While at SynthSys, Zurr, Catts and Bates initiated a research on a project on cross-kingdom cell fusion in synthetic biology between mammalian and yeast cells, to explore how the novel entities produced by these cell fusions challenge existing scientific and cultural classification systems. When borders are crossed - be they biological, geographical or conceptual - the sense of excitement and exhilaration is blended with unease.
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During their visit Zurr gave a talk at the SynthSys Open Centre, Bates gave a STIS seminar, Zurr and Catts give a public lecture at Summerhall.

Their work-in-progress was then exhibited at the Edinburgh International Science Festival (31st March - 15th April 2018) and the Western Australia Art Gallery in September 2018. The SynthSys/SymbioticA collaboration will also be the topic of a panel at the Quite Frankly Conference, which will take place at the University of Western Australia in October 2018, and opportunities will be explored for further developing this collaborative work.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/crossing-kingdoms-and-disciplines-living-art-synthsys
 
Description Sci-Screen Presentation 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A Sci-Screen event provided a light-hearted backdrop for Centre members to engage the audience of Edinburgh Skeptics in a more serious dialogue about science, its representation and its communication.

Dr Jane Calvert of SynthSys and Science, Technology and Innovation Studies, provided an introduction to media monsters and the necessity for human connectivity respectively. Synthetic Biology could be viewed as a looming technological monster - who and how do we manage this for the greater good.

Over 40 people turned up for this event which provoked a lot of heated debate.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/young-frankenstein-%E2%80%93-cautionary-tale-or-valuable-lesson
 
Description Science Art Training Workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact We welcomed Jenni Rant and the SAW Training team back to Edinburgh for our second annual training event bringing their innovative approach to teaching science to children using the power of words and pictures. This year, thanks to support from Lorna Macdonald, Principal Officer Creative Learning for Schools and Lifelong at the City of Edinburgh Council, we had great participation from local primary school teachers for the entire day. We subsequently ran workshops in seven primary schools reaching over 200 children in the Edinburgh region. This activity is in demand from teachers and children and we plan to train our local PE practitioners in the University to deliver the training.
Year(s) Of Engagement Activity 2017
URL http://www.synthsys.ed.ac.uk/news/saw-trust-inspires-second-year
 
Description Science Art Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Astrid Jaekel, a teaching Fellow and course coordinator of first year illustration at the Edinburgh College Art was keen to bring science into her classroom; the resulting - 'Long Story Short' - is based on the idea of the Illustrator becoming part of the storytelling chain. First, they absorb and process information and then they turn the resulting story into artwork that will serve as a storytelling device.

As part of a 5-week long storytelling project, first year Illustration students met with three practitioners from different fields: Master storyteller David Campbell, Sculptor Duncan Robertson and Scientist Prof Bill Earnshaw. Each gave insight into their professions and the relevance of storytelling within their practice.

The final task of the project took inspiration from scientific methods of research as well as collaborations between artists and scientists.

In response to the events of this day, students had to create an illustrated, sequential, narrative piece containing a minimum of four panels.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/science-muse
 
Description Science Art Writing Training for Schools 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact A group of 20 teachers, scientists, poets and artists went 'back to school' to learn the SAW Trust's innovative approach to teaching science with a view to applying this in schools. Over May/June they then developed and delivered innovative workshops for primary school children in five local schools. This was a great success and all schools felt that the activities enriched their teaching of the science subjects. Several schools are interested in participating again.
The activity has also enabled further engagement with key members of local education authority and Councis looking to better work with Higher Education and around the area of creativity and multidisciplinarity.
Year(s) Of Engagement Activity 2016
URL http://www.synthsys.ed.ac.uk/news/saw-trust-inspires-science-art-workshop
 
Description Science Art Writing Training for Schools 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact A group of 32 teachers, scientists, writers and artists attended to learn more about the SAW Trust's fun and innovative approach to teaching science through pictures and words.

Jenni Rant (SAW training lead and scientist) and colleagues Mike O'Driscoll (writer) and Chris Hann (poet) inspired the room with ways to explore DNA and cells using everything from pipe cleaners and paints to balloons and polystyrene balls. The 'class of 2018' excelled themselves in their creative interpretations of the cell structure.

At the end of the day, the trainers selected seven teams to develop and take workshops into schools in the Edinburgh and the Lothians. We subsequently ran workshops in 5 schools across the Edinburgh region reaching 180 children.
Year(s) Of Engagement Activity 2018
URL http://www.synthsys.ed.ac.uk/news/saw-trust-inspires-again
 
Description SynBioBeta London 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact The Centre had a joint exhibit at the London SynBioBeta conference in April 2017. This 2 day event brings together industry, investors and researchers in synthetic biology and is a flagship event for synthetic biology in the UK. Attendance > 500. Centre manager chaired a session on Synthetic Biology and Novel Materials.
Year(s) Of Engagement Activity 2017
URL http://www.synthsys.ed.ac.uk/news/synbiobeta-london-2017
 
Description Webinar: Colony picking in a fully automated DNA assembly workflow 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In this webinar Edinburgh Genome Foundry staff members described how they integrated for the first time a particular piece of equipment (a colony picker from Molecular Devices) in the workflow of automated DNA assembly. This is valuable information for researchers or industry who want to set up a similar setup and also educational for students and other audience to understand the automated workflow of DNA assembly, a key process in the growing field of synthetic biology.
Year(s) Of Engagement Activity 2017
 
Description Wigtown Big Bang Weekend 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The Big Bang Weekend is an annual event that explores different aspects of science for the public in Wigtown, Scotland's Book Town. This year the topic was 'Is it alive?' which explored what we mean by life at both large and small scales. There were great presentations on robots and artificial intelligence, whether or not there is life out there in space, and a comedian's exploration of human consciousness (or lack thereof). Centre affiliated social scientist, Dr Erika Szymanski, wowed the audience at the Big Bang Weekend in Wigtown with a sparkling presentation on yeast, its genome and how we should take better care of it. Around 80 people attended the talk and there were many questions. Erika got a lot of very positive feedback.
Year(s) Of Engagement Activity 2017
URL http://www.bbc.co.uk/news/uk-scotland-south-scotland-42902773
 
Description Workshop 'What can art, STS and synthetic biology do together?' 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Centre co-hosted a workshop with artists at the University of Western Australia to explore the intersections between art, synthetic biology and social science. It involved artists, designers and synthetic biologists from Australia, the UK and the USA.
Year(s) Of Engagement Activity 2018