Assay Development Platforms

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

Abstract

Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature and to redesign existing biological systems to perform new functions. The construction de novo of large and complex genetic circuits or metabolic pathways will enable us to for example, program stem cell differentiation, detect multiple changes in cancer cells, or engineer cell factories to produce completely novel drugs or greener chemicals and biofuels. The conventional approach of engineering cells at the bench is inherently slow and expensive. Automation and industrialization reduce development time and the economies of scale of medium to high throughput processes can reduce the cost of organism development democratising the endeavour and allowing an expansion in the number of academic groups and industries that can undertake such complex organism engineering.
To realise our ambitions for synthetic biology we need enabling technologies that can not only provide robust, reliable and cost effective methodologies for the design, construction and incorporation of synthetic DNA we need to understand the interaction of the component or pathway with the host and capture holistic datasets that report back on synthetic part and pathway performance, cell growth and health.
The initial BBSRC investment (BBM00029X1 andBBM00094X1) has helped found two DNA synthesis centres, the Edinburgh Genome Foundry (EGF, based in the School of Biological Sciences) and Liverpool GeneMill (LGM, based within the Centre for Genomic Research CGR) offering DNA design, synthesis and validation of large gene constructs (up to 1Mbp). However, we need to further expand our capabilities to include high throughput assay development suited to assessing whether the DNA construct delivers the desired output (i.e. phenotype) in the host cell. Here we request support for capital equipment that will enable us to set up multi parallel medium throughput assays for cell health, function and productivity. Alongside these platforms we build the software tools for automation and analysis, together with software to integrate this data with the design and fabrication pipelines. This will provide the data needed to inform the future design of refined DNA constructs, accelerate the design build test cycle, improve efficiency and reduce the cost of application of synthetic biology applications. Ultimately this will help drive growth of the markets than can benefit from synthetic biology and add value to the initial investment in the DNA synthesis centres.

Technical Summary

Synthetic biology has made significant strides over the past decade however, to fully realize the potential of this technology we need to be able to introduce much larger constructs to enable, for example, engineering of complete metabolic pathways or exquisite cell-control mechanisms. However, currently this requires screening a very large number of constructs to identify those that deliver the desired output. One capability missing from the arsenal of the Edinburgh and Liverpool facilities is access to automated medium throughput platforms that can swiftly screen for the desired phenotypes. This assay development capability would enable us to offer more integrated end-to-end service, help reduce the cost of delivering the desired DNA construct, and accelerate the application of synthetic biology across multiple markets.
EGF and LGM are currently automating DNA synthesis and assembly pipelines using, where possible, technology platforms that can be automated and interconnected. As the design is completely modular it can easily be expanded to include phenotype screening assays. We aim to enable the rapid design and synthesis of multiple varied DNA circuits (e.g. metabolic pathways, biosensors, counting/memory devices) and interrogate the utility of these circuits within host cell cassis via an array of assays including growth and fermentation characteristics, cell health, fluorescent reporters, RNA seq and metabolite profiling. The data generated using this battery of tests will then be processed and used to identify the best highly optimized circuits and inform design principles for the future. This vision will be achieved by adding the following screening capabilities to our already funded DNA synthesis facilities and the facilities already available at our host institutions 1. Medium throughput small volume monitored parallel cultures. 2. Metabolite screening 3. Enhanced DNA assembly platform 4. Software development.

Planned Impact

The Edinburgh Genome Foundry and Liverpool Gene Mill will provide end-to-end design, construction and phenotypic validation of large gene constructs for academic and industrial applications. The novel tool development proposed will enable the the UK to maintain a position of leadership in Synthetic Biology. This in turn will help to attract and retain high quality researchers in the UK.
We have a broad range of good working relationships with local (e.g. Ingenza, Genabler) and international businesses (e.g. Life Technologies, Selex ES, Unilever, GSK) with an interest in synthetic biology and its application and will build on these collaborations. Importantly, our existing and developing relationships with industry partners will ensure we work alongside, rather than compete with, commercial providers while safeguarding our potential to develop Intellectual Property addressing new markets. Currently there are no companies providing DNA design and synthesis with high throughput phenotypic screening in the UK so we are not competing with industry in this arena rather we are working with industry and innovating in an area which will be of great commercial interest in the future.
Close working with Edinburgh's Research & Innovations and Liverpool's Business Gateway, the Universitys' commercialization support, we allow periodic review of the commercial potential of the technology developed in the EGF and LGM.
Societal and stakeholder engagement is considered vital to the continued emergence of SB technologies as product. We wholeheartedly recognize the importance of open communication of our research to as wide an audience as possible; both through the scientific and non-scientific press, through various media outlets including the internet and through participation at specialist and general science conferences and festivals.

Publications

10 25 50
 
Description We were able to successfully downscale PCRs and the popular one-pot DNA assembly methods, Golden Gate and Gibson assemblies, from the microliter to the nanoliter scale with high assembly efficiency, which effectively cut the reagent cost by 20- to 100-fold. We envision that acoustic dispensing will become an instrumental technology in synthetic biology, in particular in the era of DNA foundries. We have published a paper in JALA describing DNA assembly using nl volumes using the Labcyte Echo machine that was JALA paper of the year. Another paper on CAD for DNA assembly is pending and a paper describing the process of DNA design through assembly and testing is in preparation. The EGF has worked in tight collaboration with Autodesk to develop Genetic Constructor (GC), an open-source web-based Computer Assisted Design tool for Synthetic Biology. The key features of GC were determined after review of existing software and customer research by the Foundry. GC makes it easy to compose new constructs and combinatorial libraries using reusable genetic parts from web registries. It allows he use of "templates" to guide in genetic constructs, and supports for large projects up to genome size. GC also allows to order a designed construct to the EGF directly from the platform, and will hopefully be a source of customers for the different Foundries. The EGF has worked on the implementation of many specialized pieces of software to assist with the robotic operations and decision-making steps of a DNA assembly process. A cloning simulator checks that the DNA parts will assemble correctly and unambiguously and predicts the final sequence. Another application selects the most adapted restriction enzymes for digestion-validation of the clones, and predicts the digestion patterns. Yet another aligns the results of sequencing with the expected sequences, generating meaningful reports to help troubleshooting. To assist with robotic operations, the EGF developed Plateo, a library featuring many parsers and protocol file generators for the different machines of the foundry, which also allows to simulate liquid handling operations so as to foresee problems such as containers being filled over capacity. All these software packages will be released in 2017 under open source licences. As a proof of concept, the EGF has assembled 96 different constructs (ranging from 7 to 25 parts) on the same plate. The process, which took around a week (including validation steps) was entirely assisted by software for the generation of picklist, data analysis, and decision making. The EGF successfully passed the admission test of the International Gene Synthesis Consortium by implementing a simple pipeline in which a sequence gets screened against a database of pathogenic proteins, as well as the NCBI database, in order to detect potentially harmful genetic constructs.
Medium throughput small volume monitored parallel cultures. The RoboLector has been fully installed and many experiments have now been run using it. It has become one of the main workhorses in the lab; experiments are run several times per week and results have been very consistent. The ability to run 48 cultures in parallel, all with separate conditions and/or sampling and induction times has been a great benefit.
The metabolomics facility has acquired a state-of-the-art Agilent 6560 Ion Mobility Quadrupole Time of Flight (IM-QTOF) mass spectrometer which is compatible with Ultra High Performance Liquid Chromatography (UHPLC), Supercritical Fluid Chromatography (SFC) and Gas Chromatography (GC). We have also acquired a GERSTEL MultiPurpose Sampler (MPS) coupled to an Agilent 7200B Gas Chromatography Quadrupole Time of Flight Mass Spectrometer (GC-QTOF).

The former is currently being used in LCMS mode. Methods already developed include the detection and relative quantitation of targeted saponins in yeast and targeted analysis of paclitaxel and structural derivatives from various modifications in bacteria. Untargeted approaches have been tested using Ostreococcus tauri as a model and can be applied to other organisms.

The GCMS is now setup to run Folch extraction and transmethylation derivatisation of fatty acids from cell pellets. Two more derivatisation protocols have been developed to target a selection of oleanolic acid derived triterpenes, simple sugars, polyols and amino acids. Extraction protocols are an on-going concern and will be optimised as projects arise. We can also detect terpenes released by bacteria into the media and trapped in a dodecane layer.

Current projects either in preliminary stages, or to be developed over the next 6-12 months include the analysis of glycans from plants, CHO cells and bacterial biofilms (LCMS), the analysis of isoprenoids in bacteria (LCMS), central carbon metabolism including glycolytic and Kreb's cycle metabolites, sugars and amino acids (LCMS and GCMS).
Exploitation Route The EGF is a facility that will be used by a wide range of academics and colleagues from industry for DNA assembly, transformation and testing of genetic constructs.
Sectors Agriculture, Food and Drink,Chemicals,Digital/Communication/Information Technologies (including Software),Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description The EGF is a facility that will be used by a wide variety of academics and industry partners for DNA assembly, transformation and testing of genetic constructs. Data from the EGF has been used by Labcyte and ThermoFisher as demonstrators of the effectiveness of their Echo systems and robotic platforms. The EGF team have hosted webinars and workshops. Due to its large scale, first of its kind and enormous integration it is still too early to assess its full economic and societal impact. However, it is clear that there is a great deal of interest in the automation of synthetic biology as evidenced by the large number of visitors from both industry and academia who want to learn more about the capabilities of the EGF and also about setting up a foundry.
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Chemicals,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
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 Crazydoc 
Description Python library (also usable via a web application on CUBA) to convert DNA sequences specified in Microsoft Word documents (such as .doc and .docx) into GENBANK or FASTA format 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Many biologists, and several customers of the Edinburgh Genome Foundry in particular, would design sequences using Microsoft Word, and highlight important features in the sequence using MS-Word's text highlighter. This makes it long and error-prone for the Foundry to convert their sequence into a format which can be processed by our software (or any other bioinformatics pipeline). Crazydoc solves this problem by directly converting a MS Word file into a Genbank record where highlights are represented as annotations. It saves our operators time and stress. 
URL https://github.com/Edinburgh-Genome-Foundry/crazydoc
 
Title DNA Cauldron 
Description An advanced cloning simulator for restriction-based assembly operations (Golden Gate, BASIC), allowing for sequence prediction, automatic part linker selection, assembly troubleshooting, etc. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact DNA Cauldron is used routinely at the Edinburgh Genome Foundry to validate customer orders and predict the final sequences of assemblies (essential for the validation step). It thus greatly accelerated the Foundry's order processing workflow. It is also being used at the London Foundry to validate orders and predict assemblies outcome. 
URL https://github.com/Edinburgh-Genome-Foundry/DnaCauldron
 
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 DNA Features Viewer 
Description A library to plot sequence annotations (e.g. from Genbank) in a flexible and customizable way, with export to various image formats. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The library powers several other EGF software projects and is used outside the EGF, mostly by bio-informaticians. 
URL https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer
 
Title EGF CUBA 
Description Collection of useful biological apps open to the general public to use (no registration required). The website counts currently 13 applications for software-assisted design, manufacturing and validation of DNA constructs. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact The website is routinely used by the members of Edinburgh Genome Foundry. By enabling Foundry customers to design and plan assemblies themselves it also reduces the planning charge of Foundry operators. The website is also used to showcase the software librairies developed at the Edinburgh Genome Foundry to other groups. 
URL http://cuba.genomefoundry.org/
 
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 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 Plateo 
Description Collection of parsers and file generators to interface with Biolab automation robots. Plateo enables to parse and write microplate data for differents robots. It also allows to parse, write, and simulate liquid transfer picklists for different robots. As of February 2018 Plateo counts 10 different parsers, and 10 different file generators, and is regularly being expanded. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Plateo underlies all robotic assembly operations at the Edinburgh Genome Foundry where it is used to translate assembly instructions into files understandable by our robots, and translate robot-generated data files from the robots (such as fragment analysis results or plate volume surveys) into human-readable format. It is also used to simulate the operations that will be run on the robots in order to ensure that no microplate well will be filled or sampled beyond its capacity, thus reducing significantly the risk of failure of the robotic operations. 
URL https://github.com/Edinburgh-Genome-Foundry/Plateo
 
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 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 Detailled overview of automated DNA assembly to biotechnology undergraduate students followed by tour around the automation setup to explain the day to day running of the foundry. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Undergraduate students (MSc) from the University of Edinburgh, who are studying biotechnology, attended this event. In a presentation the useful applications of synthetic biology were discussed. An overview was given of synthetic biology centres in the UK. It was explained, that genome foundries are needed to fulfill the technological demand the synthetic biology centres, researchers and industry will have. A lot of synthetic DNA will be needed to make the centres successful and therefore it is crucial to develop automated and standardised methods to make these high quantities with best qualities. The presentation was followed by a tour around the automated platform and detailed explanations were given. The fact that work in the foundry involves so many different disciplines seemed to be of special interest.
Year(s) Of Engagement Activity 2016,2017
 
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 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 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 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 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