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Biofoundries are a nucleating hub for industrial translation

Biofoundries are a nucleating hub for industrial translation Contemporary synthetic biology embraces the entire innovation pipeline; it is a transformative technology platform impacting new applications and improving existing industrial products and processes. However, challenges still emerge at the interface of upstream and downstream processes, integral to the value chain. It is now clear that biofoundries have a key role to play in addressing this; they provide unique and accessible infrastructure to drive the standardization necessary to deliver systematic design and engineering of biological systems and workflows. As for other biofoundries, the success of the London Biofoundry has been in part due to its expertiseinestablishingchannelsforindustrialtranslationthroughitsextensivestrategiccollaborations.Ithasalsobecomecemented as a key component of various consortia and partnerships that serve the broader bioeconomy and industrial strategies. Adopting a networked approach enables links to be made between infrastructure, researchers, industrialists and policy makers to de-risk the economic challenges of scale-up, as well as contribute to the growing bioeconomy. Key words: biofoundries; innovation; standardization; automation; commercialization Synthetic biology (also referred to as engineering biology) are developing a complete synthetic biology technology stack to embraces the entire innovation pipeline, addressing challenges deliver complex bio-design projects that are vertically integrated. thatenablethebioeconomythroughtheapplicationofbio-design Highly efficient automated manufacturing platforms, including principles. It is a transformative platform technology offering robotic liquid-handling equipment coupled with computer-aided innovative approaches for the design/redesign and fabrication of design software, enable enhanced high-throughput analyses. biological components and systems for biotechnology applica- Through such processes, biofoundries are underpinning repro- tions (1, 2). Much of the current synthetic biology activities are ducibility and enabling the quantitative precision required for focused on the rapid prototyping of biosystems to deliver novel modern biomanufacturing (3–5). A large scope of the bio-design solutions to worldwide grand challenges (3). The widespread space is also being exploited by machine learning (ML) and artifi- establishment of a community of biofoundries is seen as the cialintelligence(AI)approaches,wherebylarge-scalehigh-quality enabler for accelerating these endeavors. Biofoundries offer a data as well as proper experimental design are fundamental to unique opportunity to harness the power of constructing biology theleverageofML. Wearequicklyrecognizingthat historicalbio- with new process systems and automated workflows ( 4). At the logical data does not always meet the requirements for ML to LondonBiofoundry(LBF),wehavefocusedonearly-stagetechnol- be effective (including a lack of standardized data measurement ogy readiness levels where, through responsible innovation, we and annotation), so it is important that new data are collected have identified new materials, sustainable products, and novel and aggregated with these needs in mind. However, a major technologies that are currently being developed (5). These all challenge that still exists for researchers and biofoundries is the have the potential to revolutionize sustainable biomanufactur- enablement of high-throughput analytics and omics measure- ing - realizing the applications of synthetic biology necessitates ments, to provide the data required to feed ML and statistical the continued development of enabling technologies, with the learning approaches. This current bottleneck is preventing the polices and praxes to ensure these are accessible to the research full adoption of these approaches for bio-design and the DBTL community. cycle although many biofoundries are working to address this. Most biofoundries provide integrated molecular biology facil- In summary, biofoundry infrastructure primarily provides ities, a core laboratory extensively automated to carry out a integrated facilities for high-throughput iterative prototyping of range of workflows and with a mantra based on the synthetic biodesigns, prior to any scale-up such as a pilot-scale fermen- biologydesign-build-test-learn(DBTL)cycle.Variousbiofoundries tation or biomanufacturing (3, 5). A notable exemplar is the Submitted: 12 February 2021; Received (in revised form): 13 May 2021; Accepted: 19 May 2021 © The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Synthetic Synthetic Biolog Biology,y, 2021, 2021, VVol. ol. 66,, No No.. 11 Manchester Synthetic Biology Research Centre for Fine and Spe- to expertise and ‘know-how’ to help address-specific biotech- ciality Chemicals, where Escherichia coli strains were prototyped nology research challenges. Biofoundries can also provide these for the production of 17 chemically diverse bio-based building tools to the academic scientific community, with easy access blocks in 85days from scratch (6). to the skills and technologies required to accelerate synthetic Given that synthetic biology is a disruptive technology, it biology academic research. As such, they are janus facing, work- lends itself to commercialization via the creation of small- and ing with both academia and industry, and ideally positioned to medium-sized enterprises (SMEs) and early-stage start-up com- acceleratecommercializationandtranslationofsyntheticbiology panies (7). As an exemplar, the LBF in conjunction with Syn- technologies and applications worldwide (Figure 1; 3, 7). biCITE (the UK Innovation and Knowledge Centre for Synthetic The LBF is purposefully embedded within a hub for innova- Biology) acts as a nucleating point for a variety of biomanufac- tion and entrepreneurship (the Imperial Translation and Inno- turing applications. The LBF infrastructure has facilitated a more vation Hub) with easy access to several incubators and start-up porousinterfacebetweenindustryandacademia, withcollabora- companies (9, 10). Purposeful infrastructure integration is com- tive engagements from both sides leading to an enhanced under- monplace, another example being the Earlham Biofoundry (11). standingofthevalueeachcanbringtooneanother(seeFigure 1). Located within the Norwich Research Park, the Earlham Institute TheLBFandotherbiofoundriesnationallyandworldwidearealso has access to a thriving community of businesses, researchers leveragingupontheprogressiveculturalchangeinacademiathat and clinicians. Many of the early-stage companies are work- isrecognizingthevalueofinnovationandentrepreneurialactivity ing on a wide variety of biotechnology projects, often emerging at a curriculum level. For example, many undergraduate stu- as university start-ups that are encountering the financial and dents are now taught entrepreneurship modules and are actively logistical realities of running a technology company. Biofoundry encouragedtoengageincommercializationoftheirideasthrough infrastructure allows many of these micro-companies to rapidly multiple competitions, workshops and hackathons (8). evaluate their new ideas and biotechnology designs and obtain robust experimental data to de-risk uncertainty in their invest- ment process (Figure 1). Our own experiences of working with 1. Connecting academia with industry companies, ranging from early-stage start-ups to large tier 1 Public-funded biofoundries are generally open-access and sit at corporations and pharmaceutical companies, have allowed the the interface between academia and industry. A distinct feature development of new workflows, which can be reused to support of biofoundries is that they can be enablers for many spin-outs proof-of-concept and larger scale R&D projects. Many public- and start-up companies, by providing access to expensive infras- funded biofoundries, including the LBF, Earlham Agile, and Edin- tructure. Biofoundries can enable new companies to accelerate burgh Genome Foundry (EGF), market their technical services as the development of new products without reinventing the wheel well as educational tools such as workshops, conferences, train- every time. They can offer access to sophisticated computational ing courses and webinars. These activities have assisted many design tools, novel genetic parts, hardware and software infras- companiestodeterminehowbiofoundryinfrastructurecanfacil- tructure, bespoke workflows and assay development, in addition itatetheirowninnovationandR&Dpipelines.TheUS-basedAgile Figure 1. The biofoundry innovation ecosystem. Biofoundries act at the interface of academia and industry (gray horizontal arrows) and tap into a large array of participants and resources that contribute to ongoing technology translation and innovation in synthetic biology/biotechnology. By facilitating infrastructure access to a variety of spinouts/start-ups, SMEs and industry across the synthetic biology landscape, biofoundries create value to the innovation ecosystem. Biofoundries also provide connectivity between new synthetic biology companies with venture capitalists and private investors as well as government and policy makers (gray vertical arrows). Due to the disruptive nature of synthetic biology technologies, biofoundries also provide a focus for dialogs with other stakeholders including international policy and governance organizations (e.g. Organisation for Economic Co-operation and Development (OECD) and United Nations Convention on Biodiversity (UN-CBD)) and Non-Governmental Organisations (NGOs). T. Farzaneh and P. S. Freemont 3 Biofoundry is a distributed consortium of national labs and aca- improved standardization for these foundational technologies demicintuitions dedicated toacceleratingbiomanufacturingand (21, 22). the bioeconomy through working closely with industry (12). Sim- We view biofoundries as a key to developing and promot- ilarly, in Singapore, the SynCTI biofoundry has established major ing standards and reference materials necessary to deliver the flagship research programs and industrial network focused on promise of synthetic biology, both in terms of systematic design accelerating innovative biosolutions (13). and engineering biological systems. The unique combination of AsshowninFigure1,notonlycanbiofoundriesprovideinfras- high-throughputinfrastructureandtechnicalexpertiseinmolec- tructure access for start-ups, SMEs, larger companies and aca- ular biology, analytics, automation, engineering and software demic researchers, they can also coordinate and contribute to development provides an excellent, integrated and agile capa- activities around government policy, governance and standards. bility to quickly establish platforms for prototyping biological Internationalconsortiaofbiofoundries, liketheGBA,alsoprovide measurement standards, interoperability and developing new a wide network for knowledge exchange and training. Impor- liquid-handling workflows. The Global Biofoundry Alliance (GBA) tantly, biofoundries can also provide a gateway for public dialog isvestinginstandardssettingthroughitsmetrology,reproducibil- on the uses and applications of synthetic biology technology. ity and data quality working group activities (23). Liaison with industry by biofoundries is helping to create a framework for identifying and monitoring standardization 3. International consortia and encouraging requirements for new synthetic biology tools, technologies and reproducibility applications. Biofoundries are able to systemize an evolving list ofprioritiesthatareuniquetosyntheticbiology, includingsimple The GBA was launched at an event at the University of biological parts, the definition and adoption of new chassis, data Kobe, Japan, in May 2019. The GBA is an impressive network, standards and the development reference materials to support alreadycomprisingover30internationalbiofoundries,thatbrings the metrology of gene expression flow and also adoption costs together the world’s leading non-commercial public-funded bio- and techno-economic analysis (TEA) (14). Through the use of bio- foundries. By sharing knowledge, infrastructure and expertise, foundries, the field of synthetic biology is increasingly engaged the GBA is playing a key role accelerating the capabilities of withthescientific,technical,operationalandsemanticstandards biofoundries in exploring globally relevant and societally impact- required for the field to become a full-fledged engineering dis- ful grand challenges as well as metrology, standards setting, cipline. These developments in standards will both enable and interoperability and software developments (4, 23). accelerate the industrial translation of synthetic biology, thus ‘GlobalChallenges’isanareaofactivitywithintheGBAthatis allowing more reproducible processes governed by over-arching particularlyrelevantto thecurrentpandemic, whereexperiences regulatory requirements (15, 16). and biofoundry technology developments around COVID-19 have been shared. The GBA also provides an international forum to build a community of biofoundry practitioners and users (4, 23). 2. Standards and metrology agenda GBA biofoundries operate in an open technology environment Asanexemplar,theLBFisactivelyengagedinanIndustrialStrat- thatfacilitatesthedevelopmentofcommonstandards,andopen- egyChallengeFund(ISCF)projectwiththeNationalPhysicalLab- source reference materials, and tools across the global commu- oratory(NPL)throughtheVirtualMetrologyandStandardsCentre nity. We see these, and the associated protocols and guidelines, for Engineering Biology that was established in 2018 (17). A high- as playing an invaluable role in accelerating the application of throughput cell-free platform for intracellular measurements in synthetic biology technologies worldwide. One area of intense miniaturized format is currently being developed alongside NPL activity in the GBA, and more broadly in the synthetic biology biometrology scientists, with whom we are also generating can- field, encompasses software and data standards. Data standards didate reference materials and biosynthesis protocols (18–20). enablethereadyexchangeofinformationfromthesyntheticbiol- Through a series of workshops, we are also exploring a num- ogy workflow, allowing repositories and tools to be connected ber of key technical, regulatory and societal challenges to enable from a diversity of sources (7, 16). A key area of development is the development and adoption of standards in synthetic biology, SBOL, or the ‘Synthetic Biology Open Language’. SBOL is an open as well as how these could be implemented by our industrial standard for the representation of in silico biological design and stakeholders (14, 15). standardizes data used by synthetic biology practitioners—from Through a more extensive industrial engagement by the users to software developers to wet-lab biologists (24). broader biofoundry community, automation equipment and easy Theassociatedprotocolsandguidelinesthatareaffiliatedwith to adopt workflows have a clear role to play in addressing early- common standards, data management and reference materials stage biotechnology/synthetic biology projects. Start-up compa- acrosstheglobalcommunity,arehavingavaluableroleinshifting nies and researchers interested in starting a company need easy the mindset of young entrepreneurs. These ‘soft standards’ facil- accesstoautomationinfrastructureearlyonintheirgrowth;how- itate help the routine translation of synthetic biology, although ever, they also need advice on scale-up bioprocesses and access the industry assumption that standards may limit flexibility but to TEA expertise, as part of investor due diligence. These areas increase interoperability is also relevant. That said, we see good are not widely available in public-funded biofoundries, and these standards as increasing creativity and flexibility, because trans- gaps need to be filled quickly. One exception is the US Agile Bio- lational research objectives will be within closer reach for many foundry, where the economic feasibility of new biotechnology new start-up companies (7, 16). processes can be assessed as part of their infrastructure offer- As an exemplar, the LBF and larger synthetic biology commu- ing (12). A widespread use of biofoundries for strain engineering, nity at Imperial College recently established a collaboration with involving genetic design and DNA construction, is also allowing the US company, Riffyn, to modernize data management. Riffyn 4 Synthetic Synthetic Biolog Biology,y, 2021, 2021, VVol. ol. 66,, No No.. 11 has developed a computer-aided design approach to biotech- identification of additional funding sources and alternative fund- nology research and development that breaks down data silos ing models. For example, in the UK, the Innovate UK Smart to deliver clean, contextualized and connected data for real- Grant scheme, EPSRC Prosperity Partnerships and direct Ven- timeanalysis.Thisopen-sciencecollaborationisallowingRiffyn’s ture Capital injection (30). A collaboration led by the University cloud-based process data system to be utilized in a biofoundry of Edinburgh and the Edinburgh Genome Foundry and FUJIFIM setting. We hope the outputs of this collaboration will encourage Diosynth Biotechnologies UK (FDB) has recently won £8.7 million increasing reproducibility across the broader synthetic biology Prosperity Partnership funding to develop cost-effective ways to community, providing us with a consistent and standardized way manufacture modern antibody-based medicines (31). of sharing data both locally and externally. Having the means In the UK, smaller companies tend to organize into sector- to implement industrially proven data systems, like Riffyn, has specific clusters to enable business-to-business transactions and given us the capacity to improve the repeatability of synthetic workforce mobility (9–11). By being geographically and econom- biology research and development (25). ically accessible to such clusters or indeed facilitating the for- mation of them, biofoundries can play a specific key role in the development of metrology infrastructure to accelerate industrial 4. Repurposing synthetic biology adoption of new biotechnologies and applications (5, 11, 12, 23). technology to address global challenges Biofoundries can also play a crucial role in coordinating the The success of our biofoundry to date has been, in part, due efforts of academia, government and industry (Figure 1), through to its academic and public sector partnerships, and involve- focused meetings that foster interdisciplinary collaborations ment in other consortia that serve the broader bioeconomy (26). around shared objectives and promoting new technology devel- These recently include important collaborative projects focused opments to a wider group of stakeholders (7, 14, 17). As part of on SARS-CoV-2 testing within the Department of Infectious Dis- this, we would like to see increased interoperability, coordina- ease at Imperial, the National Health Service (NHS) Imperial tion of labor, reproducibility and reuse of people’s efforts. We Trust, the UK Dementia Research Institute and a pan-London envisage biofoundries as being central to nucleating start-ups NHS diagnostic laboratory network. By demonstrating that our and SME clusters, and drawing in the consensus of private and biofoundry infrastructure could be rapidly re-purposed and our public companies, universities and policymakers. This in turn platforms recalibrated to overcome supply chain issues, we were will facilitate the implementation of reliable, robust and afford- able to highlight the flexible and inter-operable nature of bio- able standardization of synthetic biology technologies that has foundry platform technology in a ‘real-world’ setting. The LBF’s been endorsed by a broad spectrum of synthetic biology users. workflow and open platforms are now in use in NHS pathol- Local governments and regional funding bodies could support ogy labs for frontline automated diagnostic testing in the UK such platform technologies within a biofoundry hub, to both and in other countries providing >250 000 COVID-19 tests (27). de-risk private investment in new start-ups, while also creating This partnership is a good example of how biofoundries can an active ecosystem of new companies around synthetic biology help health services around the world develop low-cost reagent- technology developments. agnosticopentestingplatforms forother infectious diseases. The LBF has extended its COVID response to include new workflows 6. Future outlook for sample pooling that can be implemented in frontline testing, aswellasHigh-Throughput(HTP)SequencingofSARS-CoV-2viral Biofoundries reflect the infrastructure required to address the variants(28).Anothernotableexampleistherapidestablishment data-rich era that contemporary biotechnology encapsulates, of a high-throughput Clinical COVID-19 Testing Service Bundle both politically and technologically. The UK biofoundry network at the DAMP Lab, increasing testing capacity to the Boston Uni- had been instrumental in engaging with policymakers, who are versity’s community (29). These exemplars illustrate the agility helping realize that a new era of bio-based production is required of biofoundries to repurpose their existing workflows for specific to drive their bioeconomies (32). Increased public investment for applications, which is one of the major strengths and unique synthetic biology research is also required, as well as further features of biofoundries. investment and upgrades for biofoundries, including staff devel- opment and retention. As industrial processes progress, we will need to implement new infrastructure to supersede the exist- 5. Sustainability and creating value ing synthetic biology technology stack to deliver on projects of Biofoundries are in a unique position to broker and manage increasing complexity and which address future challenges. The interactions between stakeholders. In publicly funded business- current pandemic has accentuated some of the weak links in led research partnerships, biofoundries are able to accelerate biosecurity preparedness and the need to develop workflows on technology readiness levels of academic research programs and automationplatformsthatcanbereadilyredeployedindiagnostic deliver economic, social and cultural prosperity. However, to laboratories (27–29). It would be wise to further establish auto- enable such partnerships, biofoundries also need to be sustain- mated high-throughput infrastructures, centered around a com- able. In our experience, the key to medium- and long-term sus- munityofpractice, involvingacademicsandindustrialistsaswell tainability is the creation of a core client base of academics and as wider stakeholders, to enable the rapid transfer and bench- industry. This can be via strategic partnerships combined with marking of biosecurity protocols on new platforms, including a flexible ‘fee-for-service’ model to deliver a variety of proof- distributed and accelerated vaccine developments. of-concept projects or collaborative research grants where costs Biofoundries of the future may not only be able to paral- for accessing the biofoundry infrastructure are included. Evalu- lelize,automateandminiaturizethestepsinthesyntheticbiology ation of the potential client base should extend beyond the host design-build-test cycles but also autonomously learn about the institute’secosystemandembracethebroadernationalandinter- design and construction of biosystems. AI and ML may narrow national research communities. While these strategies require synthetic biology’s potential design solutions to a number that significant community engagement, they can also lead to the can be efficiently generated and tested at scale. With the growth T. Farzaneh and P. S. Freemont 5 of AI and deep learning, it is plausible that design rules for con- biomanufacture of potential materials monomers. Metab. Eng., structing biological systems in specific host cells for different 60, 168–182. applications will be developed (33). In strain engineering, design 7. Clarke,L. and Kitney,R. (2020) Developing synthetic biology for rules could also consider downstream scale-up processes accel- industrial biotechnology applications. Biochem. Soc. Trans., 48, erating biomanufacturing applications. This would then allow 113–122. scientists to focus on conceptual innovations, with their ideas 8. International Genetically Engineered Machine. https://igem.org implemented rapidly in a biofoundry. (25 April 2021, date last accessed). The current climate has further highlighted a future, whereby 9. Imperial ThinkSpace. https://www.imperial.ac.uk/thinkspace/i- synthetic biology industrialists could use cloud computing to hub/ (25 April 2021, date last accessed). access more centralized biofoundries to carry out more com- 10.OpenCellLabs.https://www.opencell.bio(25April2021,datelast plex experimental workflows. We envisage a seamless interface accessed). between cloud-based upstream prototyping activities within our 11.Earlham Biofoundry. https://www.earlham.ac.uk/earlham-bio biofoundry community and downstream industrial biomanufac- foundry (25 April 2021, date last accessed). turing. In this scenario, biofoundries can be considered as a joint 12.Agile BioFoundry. https://agilebiofoundry.org (25 April 2021, date infrastructureinvestment, where many research institutions and last accessed). other stakeholder can combine their skills and funding assets. 13.SynCTI. https://syncti.org (25 April 2021, date last accessed). 14.Fostering a Synthetic Biology Standards Agenda through the Centre for Engineering Biology, Metrology and Stan- Acknowledgments dards. http://www.synbicite.com/news-events/synbicite-blog/ fostering-synthetic-biology-standards-agenda-throu/ (25 April The LBF is grateful to our collaborators from NPL and their spe- 2021, date last accessed). cialist biometrology expertise and industrial insights, in partic- 15.Beal,J., Goñi-Moreno,A., Myers,C., Hecht,A., de Vicente,M.D.C., ular Dr Max Ryadnov (NPL Fellow, Biometrology) and Dr Mike Parco,M., Schmidt,M., Timmis,K., Baldwin,G., Friedrichs,S. Adeogun (Head of Life Sciences of Health). We also thank our LBF et al. (2020) The long journey towards standards for engi- colleagues Dr Marko Storch (Head of Automation) and Dr David neering biosystems: are the molecular biology and the Bell(HeadofAnalytics),fortheirvaluabletechnicaloversightand biotech communities ready to standardise? EMBO Rep., 21, day-to-day operational expertise. e50521. 16.Beal,J., Haddock-Angelli,T., Farny,N. and Rettberg,R. (2018) Time to get serious about measurement in synthetic biology. Trends Funding Biotechnol., 36, 869–871. The London Biofoundry acknowledges support by UK Research 17.TheUKCentreforEngineeringBiology, MetrologyandStandards. and Innovation (EPSRC grants EP/L011573/1; EP/K038648/1). The https://www.npl.co.uk/projects/centre-engineering-metrology Centre of Excellence in Engineering Biology, Metrology and Stan- (25 April 2021, date last accessed). dards is funded by the Department of Business, Energy and 18.Vila-Gomez,P., Noble,J.E. and Ryadnov,M.G. 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Biofoundries are a nucleating hub for industrial translation

Synthetic Biology , Volume 6 (1): 1 – Jun 23, 2021

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Oxford University Press
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© The Author(s) 2021. Published by Oxford University Press.
eISSN
2397-7000
DOI
10.1093/synbio/ysab013
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Abstract

Contemporary synthetic biology embraces the entire innovation pipeline; it is a transformative technology platform impacting new applications and improving existing industrial products and processes. However, challenges still emerge at the interface of upstream and downstream processes, integral to the value chain. It is now clear that biofoundries have a key role to play in addressing this; they provide unique and accessible infrastructure to drive the standardization necessary to deliver systematic design and engineering of biological systems and workflows. As for other biofoundries, the success of the London Biofoundry has been in part due to its expertiseinestablishingchannelsforindustrialtranslationthroughitsextensivestrategiccollaborations.Ithasalsobecomecemented as a key component of various consortia and partnerships that serve the broader bioeconomy and industrial strategies. Adopting a networked approach enables links to be made between infrastructure, researchers, industrialists and policy makers to de-risk the economic challenges of scale-up, as well as contribute to the growing bioeconomy. Key words: biofoundries; innovation; standardization; automation; commercialization Synthetic biology (also referred to as engineering biology) are developing a complete synthetic biology technology stack to embraces the entire innovation pipeline, addressing challenges deliver complex bio-design projects that are vertically integrated. thatenablethebioeconomythroughtheapplicationofbio-design Highly efficient automated manufacturing platforms, including principles. It is a transformative platform technology offering robotic liquid-handling equipment coupled with computer-aided innovative approaches for the design/redesign and fabrication of design software, enable enhanced high-throughput analyses. biological components and systems for biotechnology applica- Through such processes, biofoundries are underpinning repro- tions (1, 2). Much of the current synthetic biology activities are ducibility and enabling the quantitative precision required for focused on the rapid prototyping of biosystems to deliver novel modern biomanufacturing (3–5). A large scope of the bio-design solutions to worldwide grand challenges (3). The widespread space is also being exploited by machine learning (ML) and artifi- establishment of a community of biofoundries is seen as the cialintelligence(AI)approaches,wherebylarge-scalehigh-quality enabler for accelerating these endeavors. Biofoundries offer a data as well as proper experimental design are fundamental to unique opportunity to harness the power of constructing biology theleverageofML. Wearequicklyrecognizingthat historicalbio- with new process systems and automated workflows ( 4). At the logical data does not always meet the requirements for ML to LondonBiofoundry(LBF),wehavefocusedonearly-stagetechnol- be effective (including a lack of standardized data measurement ogy readiness levels where, through responsible innovation, we and annotation), so it is important that new data are collected have identified new materials, sustainable products, and novel and aggregated with these needs in mind. However, a major technologies that are currently being developed (5). These all challenge that still exists for researchers and biofoundries is the have the potential to revolutionize sustainable biomanufactur- enablement of high-throughput analytics and omics measure- ing - realizing the applications of synthetic biology necessitates ments, to provide the data required to feed ML and statistical the continued development of enabling technologies, with the learning approaches. This current bottleneck is preventing the polices and praxes to ensure these are accessible to the research full adoption of these approaches for bio-design and the DBTL community. cycle although many biofoundries are working to address this. Most biofoundries provide integrated molecular biology facil- In summary, biofoundry infrastructure primarily provides ities, a core laboratory extensively automated to carry out a integrated facilities for high-throughput iterative prototyping of range of workflows and with a mantra based on the synthetic biodesigns, prior to any scale-up such as a pilot-scale fermen- biologydesign-build-test-learn(DBTL)cycle.Variousbiofoundries tation or biomanufacturing (3, 5). A notable exemplar is the Submitted: 12 February 2021; Received (in revised form): 13 May 2021; Accepted: 19 May 2021 © The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Synthetic Synthetic Biolog Biology,y, 2021, 2021, VVol. ol. 66,, No No.. 11 Manchester Synthetic Biology Research Centre for Fine and Spe- to expertise and ‘know-how’ to help address-specific biotech- ciality Chemicals, where Escherichia coli strains were prototyped nology research challenges. Biofoundries can also provide these for the production of 17 chemically diverse bio-based building tools to the academic scientific community, with easy access blocks in 85days from scratch (6). to the skills and technologies required to accelerate synthetic Given that synthetic biology is a disruptive technology, it biology academic research. As such, they are janus facing, work- lends itself to commercialization via the creation of small- and ing with both academia and industry, and ideally positioned to medium-sized enterprises (SMEs) and early-stage start-up com- acceleratecommercializationandtranslationofsyntheticbiology panies (7). As an exemplar, the LBF in conjunction with Syn- technologies and applications worldwide (Figure 1; 3, 7). biCITE (the UK Innovation and Knowledge Centre for Synthetic The LBF is purposefully embedded within a hub for innova- Biology) acts as a nucleating point for a variety of biomanufac- tion and entrepreneurship (the Imperial Translation and Inno- turing applications. The LBF infrastructure has facilitated a more vation Hub) with easy access to several incubators and start-up porousinterfacebetweenindustryandacademia, withcollabora- companies (9, 10). Purposeful infrastructure integration is com- tive engagements from both sides leading to an enhanced under- monplace, another example being the Earlham Biofoundry (11). standingofthevalueeachcanbringtooneanother(seeFigure 1). Located within the Norwich Research Park, the Earlham Institute TheLBFandotherbiofoundriesnationallyandworldwidearealso has access to a thriving community of businesses, researchers leveragingupontheprogressiveculturalchangeinacademiathat and clinicians. Many of the early-stage companies are work- isrecognizingthevalueofinnovationandentrepreneurialactivity ing on a wide variety of biotechnology projects, often emerging at a curriculum level. For example, many undergraduate stu- as university start-ups that are encountering the financial and dents are now taught entrepreneurship modules and are actively logistical realities of running a technology company. Biofoundry encouragedtoengageincommercializationoftheirideasthrough infrastructure allows many of these micro-companies to rapidly multiple competitions, workshops and hackathons (8). evaluate their new ideas and biotechnology designs and obtain robust experimental data to de-risk uncertainty in their invest- ment process (Figure 1). Our own experiences of working with 1. Connecting academia with industry companies, ranging from early-stage start-ups to large tier 1 Public-funded biofoundries are generally open-access and sit at corporations and pharmaceutical companies, have allowed the the interface between academia and industry. A distinct feature development of new workflows, which can be reused to support of biofoundries is that they can be enablers for many spin-outs proof-of-concept and larger scale R&D projects. Many public- and start-up companies, by providing access to expensive infras- funded biofoundries, including the LBF, Earlham Agile, and Edin- tructure. Biofoundries can enable new companies to accelerate burgh Genome Foundry (EGF), market their technical services as the development of new products without reinventing the wheel well as educational tools such as workshops, conferences, train- every time. They can offer access to sophisticated computational ing courses and webinars. These activities have assisted many design tools, novel genetic parts, hardware and software infras- companiestodeterminehowbiofoundryinfrastructurecanfacil- tructure, bespoke workflows and assay development, in addition itatetheirowninnovationandR&Dpipelines.TheUS-basedAgile Figure 1. The biofoundry innovation ecosystem. Biofoundries act at the interface of academia and industry (gray horizontal arrows) and tap into a large array of participants and resources that contribute to ongoing technology translation and innovation in synthetic biology/biotechnology. By facilitating infrastructure access to a variety of spinouts/start-ups, SMEs and industry across the synthetic biology landscape, biofoundries create value to the innovation ecosystem. Biofoundries also provide connectivity between new synthetic biology companies with venture capitalists and private investors as well as government and policy makers (gray vertical arrows). Due to the disruptive nature of synthetic biology technologies, biofoundries also provide a focus for dialogs with other stakeholders including international policy and governance organizations (e.g. Organisation for Economic Co-operation and Development (OECD) and United Nations Convention on Biodiversity (UN-CBD)) and Non-Governmental Organisations (NGOs). T. Farzaneh and P. S. Freemont 3 Biofoundry is a distributed consortium of national labs and aca- improved standardization for these foundational technologies demicintuitions dedicated toacceleratingbiomanufacturingand (21, 22). the bioeconomy through working closely with industry (12). Sim- We view biofoundries as a key to developing and promot- ilarly, in Singapore, the SynCTI biofoundry has established major ing standards and reference materials necessary to deliver the flagship research programs and industrial network focused on promise of synthetic biology, both in terms of systematic design accelerating innovative biosolutions (13). and engineering biological systems. The unique combination of AsshowninFigure1,notonlycanbiofoundriesprovideinfras- high-throughputinfrastructureandtechnicalexpertiseinmolec- tructure access for start-ups, SMEs, larger companies and aca- ular biology, analytics, automation, engineering and software demic researchers, they can also coordinate and contribute to development provides an excellent, integrated and agile capa- activities around government policy, governance and standards. bility to quickly establish platforms for prototyping biological Internationalconsortiaofbiofoundries, liketheGBA,alsoprovide measurement standards, interoperability and developing new a wide network for knowledge exchange and training. Impor- liquid-handling workflows. The Global Biofoundry Alliance (GBA) tantly, biofoundries can also provide a gateway for public dialog isvestinginstandardssettingthroughitsmetrology,reproducibil- on the uses and applications of synthetic biology technology. ity and data quality working group activities (23). Liaison with industry by biofoundries is helping to create a framework for identifying and monitoring standardization 3. International consortia and encouraging requirements for new synthetic biology tools, technologies and reproducibility applications. Biofoundries are able to systemize an evolving list ofprioritiesthatareuniquetosyntheticbiology, includingsimple The GBA was launched at an event at the University of biological parts, the definition and adoption of new chassis, data Kobe, Japan, in May 2019. The GBA is an impressive network, standards and the development reference materials to support alreadycomprisingover30internationalbiofoundries,thatbrings the metrology of gene expression flow and also adoption costs together the world’s leading non-commercial public-funded bio- and techno-economic analysis (TEA) (14). Through the use of bio- foundries. By sharing knowledge, infrastructure and expertise, foundries, the field of synthetic biology is increasingly engaged the GBA is playing a key role accelerating the capabilities of withthescientific,technical,operationalandsemanticstandards biofoundries in exploring globally relevant and societally impact- required for the field to become a full-fledged engineering dis- ful grand challenges as well as metrology, standards setting, cipline. These developments in standards will both enable and interoperability and software developments (4, 23). accelerate the industrial translation of synthetic biology, thus ‘GlobalChallenges’isanareaofactivitywithintheGBAthatis allowing more reproducible processes governed by over-arching particularlyrelevantto thecurrentpandemic, whereexperiences regulatory requirements (15, 16). and biofoundry technology developments around COVID-19 have been shared. The GBA also provides an international forum to build a community of biofoundry practitioners and users (4, 23). 2. Standards and metrology agenda GBA biofoundries operate in an open technology environment Asanexemplar,theLBFisactivelyengagedinanIndustrialStrat- thatfacilitatesthedevelopmentofcommonstandards,andopen- egyChallengeFund(ISCF)projectwiththeNationalPhysicalLab- source reference materials, and tools across the global commu- oratory(NPL)throughtheVirtualMetrologyandStandardsCentre nity. We see these, and the associated protocols and guidelines, for Engineering Biology that was established in 2018 (17). A high- as playing an invaluable role in accelerating the application of throughput cell-free platform for intracellular measurements in synthetic biology technologies worldwide. One area of intense miniaturized format is currently being developed alongside NPL activity in the GBA, and more broadly in the synthetic biology biometrology scientists, with whom we are also generating can- field, encompasses software and data standards. Data standards didate reference materials and biosynthesis protocols (18–20). enablethereadyexchangeofinformationfromthesyntheticbiol- Through a series of workshops, we are also exploring a num- ogy workflow, allowing repositories and tools to be connected ber of key technical, regulatory and societal challenges to enable from a diversity of sources (7, 16). A key area of development is the development and adoption of standards in synthetic biology, SBOL, or the ‘Synthetic Biology Open Language’. SBOL is an open as well as how these could be implemented by our industrial standard for the representation of in silico biological design and stakeholders (14, 15). standardizes data used by synthetic biology practitioners—from Through a more extensive industrial engagement by the users to software developers to wet-lab biologists (24). broader biofoundry community, automation equipment and easy Theassociatedprotocolsandguidelinesthatareaffiliatedwith to adopt workflows have a clear role to play in addressing early- common standards, data management and reference materials stage biotechnology/synthetic biology projects. Start-up compa- acrosstheglobalcommunity,arehavingavaluableroleinshifting nies and researchers interested in starting a company need easy the mindset of young entrepreneurs. These ‘soft standards’ facil- accesstoautomationinfrastructureearlyonintheirgrowth;how- itate help the routine translation of synthetic biology, although ever, they also need advice on scale-up bioprocesses and access the industry assumption that standards may limit flexibility but to TEA expertise, as part of investor due diligence. These areas increase interoperability is also relevant. That said, we see good are not widely available in public-funded biofoundries, and these standards as increasing creativity and flexibility, because trans- gaps need to be filled quickly. One exception is the US Agile Bio- lational research objectives will be within closer reach for many foundry, where the economic feasibility of new biotechnology new start-up companies (7, 16). processes can be assessed as part of their infrastructure offer- As an exemplar, the LBF and larger synthetic biology commu- ing (12). A widespread use of biofoundries for strain engineering, nity at Imperial College recently established a collaboration with involving genetic design and DNA construction, is also allowing the US company, Riffyn, to modernize data management. Riffyn 4 Synthetic Synthetic Biolog Biology,y, 2021, 2021, VVol. ol. 66,, No No.. 11 has developed a computer-aided design approach to biotech- identification of additional funding sources and alternative fund- nology research and development that breaks down data silos ing models. For example, in the UK, the Innovate UK Smart to deliver clean, contextualized and connected data for real- Grant scheme, EPSRC Prosperity Partnerships and direct Ven- timeanalysis.Thisopen-sciencecollaborationisallowingRiffyn’s ture Capital injection (30). A collaboration led by the University cloud-based process data system to be utilized in a biofoundry of Edinburgh and the Edinburgh Genome Foundry and FUJIFIM setting. We hope the outputs of this collaboration will encourage Diosynth Biotechnologies UK (FDB) has recently won £8.7 million increasing reproducibility across the broader synthetic biology Prosperity Partnership funding to develop cost-effective ways to community, providing us with a consistent and standardized way manufacture modern antibody-based medicines (31). of sharing data both locally and externally. Having the means In the UK, smaller companies tend to organize into sector- to implement industrially proven data systems, like Riffyn, has specific clusters to enable business-to-business transactions and given us the capacity to improve the repeatability of synthetic workforce mobility (9–11). By being geographically and econom- biology research and development (25). ically accessible to such clusters or indeed facilitating the for- mation of them, biofoundries can play a specific key role in the development of metrology infrastructure to accelerate industrial 4. Repurposing synthetic biology adoption of new biotechnologies and applications (5, 11, 12, 23). technology to address global challenges Biofoundries can also play a crucial role in coordinating the The success of our biofoundry to date has been, in part, due efforts of academia, government and industry (Figure 1), through to its academic and public sector partnerships, and involve- focused meetings that foster interdisciplinary collaborations ment in other consortia that serve the broader bioeconomy (26). around shared objectives and promoting new technology devel- These recently include important collaborative projects focused opments to a wider group of stakeholders (7, 14, 17). As part of on SARS-CoV-2 testing within the Department of Infectious Dis- this, we would like to see increased interoperability, coordina- ease at Imperial, the National Health Service (NHS) Imperial tion of labor, reproducibility and reuse of people’s efforts. We Trust, the UK Dementia Research Institute and a pan-London envisage biofoundries as being central to nucleating start-ups NHS diagnostic laboratory network. By demonstrating that our and SME clusters, and drawing in the consensus of private and biofoundry infrastructure could be rapidly re-purposed and our public companies, universities and policymakers. This in turn platforms recalibrated to overcome supply chain issues, we were will facilitate the implementation of reliable, robust and afford- able to highlight the flexible and inter-operable nature of bio- able standardization of synthetic biology technologies that has foundry platform technology in a ‘real-world’ setting. The LBF’s been endorsed by a broad spectrum of synthetic biology users. workflow and open platforms are now in use in NHS pathol- Local governments and regional funding bodies could support ogy labs for frontline automated diagnostic testing in the UK such platform technologies within a biofoundry hub, to both and in other countries providing >250 000 COVID-19 tests (27). de-risk private investment in new start-ups, while also creating This partnership is a good example of how biofoundries can an active ecosystem of new companies around synthetic biology help health services around the world develop low-cost reagent- technology developments. agnosticopentestingplatforms forother infectious diseases. The LBF has extended its COVID response to include new workflows 6. Future outlook for sample pooling that can be implemented in frontline testing, aswellasHigh-Throughput(HTP)SequencingofSARS-CoV-2viral Biofoundries reflect the infrastructure required to address the variants(28).Anothernotableexampleistherapidestablishment data-rich era that contemporary biotechnology encapsulates, of a high-throughput Clinical COVID-19 Testing Service Bundle both politically and technologically. The UK biofoundry network at the DAMP Lab, increasing testing capacity to the Boston Uni- had been instrumental in engaging with policymakers, who are versity’s community (29). These exemplars illustrate the agility helping realize that a new era of bio-based production is required of biofoundries to repurpose their existing workflows for specific to drive their bioeconomies (32). Increased public investment for applications, which is one of the major strengths and unique synthetic biology research is also required, as well as further features of biofoundries. investment and upgrades for biofoundries, including staff devel- opment and retention. As industrial processes progress, we will need to implement new infrastructure to supersede the exist- 5. Sustainability and creating value ing synthetic biology technology stack to deliver on projects of Biofoundries are in a unique position to broker and manage increasing complexity and which address future challenges. The interactions between stakeholders. In publicly funded business- current pandemic has accentuated some of the weak links in led research partnerships, biofoundries are able to accelerate biosecurity preparedness and the need to develop workflows on technology readiness levels of academic research programs and automationplatformsthatcanbereadilyredeployedindiagnostic deliver economic, social and cultural prosperity. However, to laboratories (27–29). It would be wise to further establish auto- enable such partnerships, biofoundries also need to be sustain- mated high-throughput infrastructures, centered around a com- able. In our experience, the key to medium- and long-term sus- munityofpractice, involvingacademicsandindustrialistsaswell tainability is the creation of a core client base of academics and as wider stakeholders, to enable the rapid transfer and bench- industry. This can be via strategic partnerships combined with marking of biosecurity protocols on new platforms, including a flexible ‘fee-for-service’ model to deliver a variety of proof- distributed and accelerated vaccine developments. of-concept projects or collaborative research grants where costs Biofoundries of the future may not only be able to paral- for accessing the biofoundry infrastructure are included. Evalu- lelize,automateandminiaturizethestepsinthesyntheticbiology ation of the potential client base should extend beyond the host design-build-test cycles but also autonomously learn about the institute’secosystemandembracethebroadernationalandinter- design and construction of biosystems. AI and ML may narrow national research communities. While these strategies require synthetic biology’s potential design solutions to a number that significant community engagement, they can also lead to the can be efficiently generated and tested at scale. With the growth T. Farzaneh and P. S. 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Journal

Synthetic BiologyOxford University Press

Published: Jun 23, 2021

Keywords: biofoundries; innovation; standardization; automation; commercialization

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