OpenBioMAPS: shared tools for accelerating UK bio-manufacturing
Lead Research Organisation:
University of Cambridge
Department Name: Plant Sciences
Abstract
We will develop an ecosystem of open source tools to accelerate adoption of engineering biology capabilities in the UK biomanufacturing sector. IP protection allows bioenterprises freedom to operate and prevent unfair competition. However, most engineered biosystems require many "nuts- and-bolts" parts. Start-ups and SMEs, who are critical to advance UK clean growth targets through novel sustainable manufacturing processes, have limited access compared to established companies and may need to negotiate a thicket of licences.
Open licensing can reduce transaction costs in adoption of new innovations by SME's, as we demonstrated in the OpenPlant research centre. We will now expand our previous work developing DNA toolkits for plant and microbial engineering (openplant.org), legal tools for materials sharing (OpenMTA.org) and training for engineering and biology (e.g. biomaker.org). We plan to develop (i) biological engineering tools for UK bio-manufacturing companies including prototypes for microbial fermentation and plant chloroplast-based bioproduction and opportunities for commercialisation, (ii) training for academics and industry scientists to develop skills at the interface of biology and engineering; iii) mini-projects across the UK engineering biology community to promote further development of tools. Overall, this will build capacity for adoption of open source tools, principles and development practices.
Open source tools are pervasive in computing, industry estimates suggest that 80-90% of new apps are built from existing components, mostly open source. Biomanufacturing could benefit from similar reusability. We aim to establish a flagship platform to accelerate the UK biomanufacturing enterprise, and a possible springboard for establishing an Open Source Program Office (OSPO) for UK engineering biology, mirroring successful tech industry OSPOs.
Open licensing can reduce transaction costs in adoption of new innovations by SME's, as we demonstrated in the OpenPlant research centre. We will now expand our previous work developing DNA toolkits for plant and microbial engineering (openplant.org), legal tools for materials sharing (OpenMTA.org) and training for engineering and biology (e.g. biomaker.org). We plan to develop (i) biological engineering tools for UK bio-manufacturing companies including prototypes for microbial fermentation and plant chloroplast-based bioproduction and opportunities for commercialisation, (ii) training for academics and industry scientists to develop skills at the interface of biology and engineering; iii) mini-projects across the UK engineering biology community to promote further development of tools. Overall, this will build capacity for adoption of open source tools, principles and development practices.
Open source tools are pervasive in computing, industry estimates suggest that 80-90% of new apps are built from existing components, mostly open source. Biomanufacturing could benefit from similar reusability. We aim to establish a flagship platform to accelerate the UK biomanufacturing enterprise, and a possible springboard for establishing an Open Source Program Office (OSPO) for UK engineering biology, mirroring successful tech industry OSPOs.
Technical Summary
OpenBioMAPS addresses Engineering Biology for clean growth. Specifically we are developing open source tools for distributed biomanufacturing of enzymes and antibodies at low-cost using benchtop Microbial and Plant systems, with routes to scale-up for industrial plant-based production in chloroplasts. This includes a collection of i) innovative DNA toolkits for protein expression in Escherichia coli, Pichia pastoris and Marchantia polymorpha chloroplasts; ii) open strains that can be freely distributed for commercial use; iii) accompanying bioreactor and bioprocessing sensor designs that will enable UK startups and SMEs to rapidly establish protein biomanufacturing workflows with low capital expenditure.
In parallel we will work with UK biomanufacturing startups and SMEs to better understand their needs and develop a community of developers and users of open biomanufacturing tools; create training for academics and industry scientists to develop skills at the interface of biology and engineering; and run mini-projects across the UK engineering biology community to promote further development of tools. Overall, this will build capacity for adoption of open source biomanufacturing tools, principles and development practices.
Our ultimate goal is to leverage advancements in synthetic biology to reduce financial and transactional costs of microbial and plant-based protein production for researchers and innovators, ensure freedom to operate and accelerate the UK's transition to a sustainable bioeconomy.
In parallel we will work with UK biomanufacturing startups and SMEs to better understand their needs and develop a community of developers and users of open biomanufacturing tools; create training for academics and industry scientists to develop skills at the interface of biology and engineering; and run mini-projects across the UK engineering biology community to promote further development of tools. Overall, this will build capacity for adoption of open source biomanufacturing tools, principles and development practices.
Our ultimate goal is to leverage advancements in synthetic biology to reduce financial and transactional costs of microbial and plant-based protein production for researchers and innovators, ensure freedom to operate and accelerate the UK's transition to a sustainable bioeconomy.
Publications
Tse SW
(2024)
Optimizing Promoters and Subcellular Localization for Constitutive Transgene Expression in Marchantia polymorpha.
in Plant & cell physiology
| Description | The objective of the OpenBioMAPS project is to develop an ecosystem of open source tools to accelerate adoption of engineering biology capabilities in the UK biomanufacturing sector. This project involves developing a collection of: (i) innovative DNA toolkits for protein expression in Escherichia coli, Pichia pastoris and Marchantia polymorpha chloroplasts (WP1, Objective 1.1; WP2, Objective 2.1, 2.3); (ii) open protein expressing strains that can be freely distributed for commercial use (WP1, Objective 1.2); (iii) bioreactor and bioprocessing designs that will enable UK startups and small/medium enterprises (SMEs) to rapidly establish protein biomanufacturing workflows with low capital expenditure (WP3, Objective 3.1). In parallel we will work with UK biomanufacturing startups and SMEs to better understand their needs for next-generation, affordable technologies (WP4, Objective 4.1); seed a community of developers and users of open biomanufacturing tools (WP4, Objective 4.2); create training for academics and industry scientists to develop skills at the interface of biology and engineering (WP3, Objective 3.1); and use this as a springboard to run interdisciplinary mini-projects across the UK engineering biology community. Overall, this will build capacity for adoption of open source biomanufacturing tools and development practices. WP1 involves developing innovative DNA toolkits for protein expression in Escherichia coli and Pichia pastoris, and open protein expressing strains that can be freely distributed for commercial use. We have adapted a subset of the Open DNA Collections to the Reclone protein expression cassette DNA assembly syntax and sequence-validated those DNA parts (work in progress, towards Milestone M1.1). We have also established IP-free protocols for expression cassette assembly through genetic recombineering in E. coli, and are currently focused on producing the intended protein expression strain (towards Milestone M1.3). WP2 involves the engineering of Marchantia polymorpha chloroplasts as a simple plant-based system for farming recombinant proteins. Since the start of the project and appointment of Dr Ravendran Vasudevan (cyanobacterial and chloroplast engineering) and Rory Harrison (industrial bioproduction), we have made progress on a number of fronts. (i) The first generation of target genes have been cloned into transformation vectors, sequence verified, biolistically transformed and transgenic plant lines were selected (Tasks 2.1.1-3). Characterisation of the lines has started, with a range of protein cargoes: fluorescent markers, synthetic nanobodies and tag/capture elements for large-scale affinity purification based on subtilisin and its prodomain. (ii) We have continued to improve methods of hydroponic culture for large-scale propagation of plant material. This includes use of industry-suitable large trays and lower-cost, lower-maintenance irrigation methods (Task 2.3.1). (iii) Long-range PCR is being used as a short-cut for assembly of larger transforming DNAs, with parts of 20-30Kb in size, and currently experimenting with whole genome assembly and delivery to increase the speed and accessibility of this part of the work (Task 2.1.1). (iv) We have constructed, validated and tested modified versions of the Marchantia chloroplast genome, removing inverted repeat domains for development of shuttle vectors and more efficient transformation vectors. (v) Synthesis and assembly of the second round of industrially relevant protein targets is underway. These include stabilised, protein-engineered versions of growth factors and serum components. WP3 aims to generate novel hardware for biomanufacturing, and to share tools and training materials for building customisations and new bioinstrumentation designs - as a mechanism for fostering capacity for interdisciplinary collaboration in engineering biology, and for growing a community of tool developers. We have an established web-based platform for sharing technical information, including a Beginner's Handbook for no-code development of bioinstrumentation, including a wide range of training materials. We have now selected a new generation of electronic hardware and compatible software to extend these materials into more advanced applications, while retaining the ability to use no-code tools. The new hardware is ESP32-S3 based and includes improved capabilities for video capture and communications, along with an advanced touchscreen display module that is well-suited to fast, code-free prototyping - while maintaining low cost, and ability to rapidly convert a prototype into a robust hard-wired device (Task 3.1.1). We are currently preparing an Advanced Handbook in preparation for training workshops planned this year. In WP4, we are working to create and strengthen links between UK academia and industry, as a foundation for reducing barriers to adopting open-source technologies for biomanufacturing, such as the tools that will be developed in WP1 and WP2. The initial objective is to understand the barriers faced by UK startups and SMEs in using biomanufacturing to address clean growth and biomedical mission areas (towards WP4, Objective 4.1.1). We are focusing in particular on challenges in recombinant protein production on a lab-scale through to industrial levels, and in areas related to (i) technical challenges, (ii) access to technologies, and (iii) intellectual property. To date, we have contacted 25 companies and/or individuals within the biomanufacturing sector to request interviews for understanding their challenges. We have conducted interviews with three, and have two scheduled by end of March 2025. Analysis of the interviews will help inform the direction of WP1 in the development of the open microbial expression toolkits and strains. |
| Exploitation Route | WP1, WP3, and WP4 include activities that provide open access to technologies and that foster engagement with multi-disciplinary communities, including synthetic biologists, industry professionals, social scientists and students through a combination of online resources, interactive workshops and forums. This will maximise adoption and reuse of OpenBioMAPS outputs, and opportunities to deliver economic and societal impacts from innovation in biomanufacturing models. The open/free-use DNA toolkits and the E. coli expression strain produced by WP1 are intended for distribution among interested biotechnology companies in the UK. Additionally, we are at the early stage of collaborating with Addgene, a non-profit plasmid repository, and Cell Repo, an online strain database, who will be able to make the tools and strains that we develop more accessible to those who wish to use these tools for protein production and further development of the strains for commercial purposes. We will also report upon these outputs and hold open biomanufacturing workshops as part of WP4 in order to showcase and support UK startups and SMEs in making use of these open resources. |
| Sectors | Agriculture Food and Drink Education Electronics Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | WP1-4 are in progress, we would not expect our findings to have been used by others at this point. |
| First Year Of Impact | 2024 |
| Description | Reclone Network: open biological reagents for biomedical research |
| Organisation | Cayetano Heredia University |
| Country | Peru |
| Sector | Academic/University |
| PI Contribution | In discussions with the global Reclone Hub leads, our team submitted information for a Request for Information to the Open Science Team at the Chan Zuckerberg Initiative in Mar-2024, and was subsequently approached to submit a proposal on accelerating the uptake and implementation of open science best practices. As Reclone was established from the Open Bioeconomy Lab at the University of Cambridge, we provide support and guidance to the Regional Hubs in the producing and distributing the Open DNA Collections/toolkits to the Hubs for redistribution. Development of the toolkits will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines), which in turn helps to inform the potential users (startups and SMEs) in the UK biomanufacturing sector. |
| Collaborator Contribution | We partnered up with the Reclone Hub in Latin America - led by Prof María Teresa Damiani - to take the lead on this proposal and she was awarded $300,000 over two years (starting Feb-2025) to strengthen the Reclone Regional Hub in Argentina and establish new nodes in Chile and Peru. This aims to empower local labs with the tools and training to produce lab chemicals autonomously, enabling faster, cheaper, and more reliable research. The funding primarily supports researchers in Latin America to further develop the Open DNA Collections, which will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines) to enable research globally. For more information: https://www.science.org/content/article/scientists-latin-america-struggle-get-key-chemicals-and-other-reagents-experiments |
| Impact | Proposal only recently awarded and are in the early stages of sharing resources between UK and Argentina, and formalising plans for developing and subsequently sharing the updated Open DNA Collections. |
| Start Year | 2024 |
| Description | Reclone Network: open biological reagents for biomedical research |
| Organisation | National University of Cuyo |
| Country | Argentina |
| Sector | Academic/University |
| PI Contribution | In discussions with the global Reclone Hub leads, our team submitted information for a Request for Information to the Open Science Team at the Chan Zuckerberg Initiative in Mar-2024, and was subsequently approached to submit a proposal on accelerating the uptake and implementation of open science best practices. As Reclone was established from the Open Bioeconomy Lab at the University of Cambridge, we provide support and guidance to the Regional Hubs in the producing and distributing the Open DNA Collections/toolkits to the Hubs for redistribution. Development of the toolkits will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines), which in turn helps to inform the potential users (startups and SMEs) in the UK biomanufacturing sector. |
| Collaborator Contribution | We partnered up with the Reclone Hub in Latin America - led by Prof María Teresa Damiani - to take the lead on this proposal and she was awarded $300,000 over two years (starting Feb-2025) to strengthen the Reclone Regional Hub in Argentina and establish new nodes in Chile and Peru. This aims to empower local labs with the tools and training to produce lab chemicals autonomously, enabling faster, cheaper, and more reliable research. The funding primarily supports researchers in Latin America to further develop the Open DNA Collections, which will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines) to enable research globally. For more information: https://www.science.org/content/article/scientists-latin-america-struggle-get-key-chemicals-and-other-reagents-experiments |
| Impact | Proposal only recently awarded and are in the early stages of sharing resources between UK and Argentina, and formalising plans for developing and subsequently sharing the updated Open DNA Collections. |
| Start Year | 2024 |
| Description | Reclone Network: open biological reagents for biomedical research |
| Organisation | National University of Cuyo |
| Country | Argentina |
| Sector | Academic/University |
| PI Contribution | In discussions with the global Reclone Hub leads, our team submitted information for a Request for Information to the Open Science Team at the Chan Zuckerberg Initiative in Mar-2024, and was subsequently approached to submit a proposal on accelerating the uptake and implementation of open science best practices. As Reclone was established from the Open Bioeconomy Lab at the University of Cambridge, we provide support and guidance to the Regional Hubs in the producing and distributing the Open DNA Collections/toolkits to the Hubs for redistribution. Development of the toolkits will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines), which in turn helps to inform the potential users (startups and SMEs) in the UK biomanufacturing sector. |
| Collaborator Contribution | We partnered up with the Reclone Hub in Latin America - led by Prof María Teresa Damiani - to take the lead on this proposal and she was awarded $300,000 over two years (starting Feb-2025) to strengthen the Reclone Regional Hub in Argentina and establish new nodes in Chile and Peru. This aims to empower local labs with the tools and training to produce lab chemicals autonomously, enabling faster, cheaper, and more reliable research. The funding primarily supports researchers in Latin America to further develop the Open DNA Collections, which will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines) to enable research globally. For more information: https://www.science.org/content/article/scientists-latin-america-struggle-get-key-chemicals-and-other-reagents-experiments |
| Impact | Proposal only recently awarded and are in the early stages of sharing resources between UK and Argentina, and formalising plans for developing and subsequently sharing the updated Open DNA Collections. |
| Start Year | 2024 |
| Description | Reclone Network: open biological reagents for biomedical research |
| Organisation | Pontifical Catholic University of Chile |
| Country | Chile |
| Sector | Academic/University |
| PI Contribution | In discussions with the global Reclone Hub leads, our team submitted information for a Request for Information to the Open Science Team at the Chan Zuckerberg Initiative in Mar-2024, and was subsequently approached to submit a proposal on accelerating the uptake and implementation of open science best practices. As Reclone was established from the Open Bioeconomy Lab at the University of Cambridge, we provide support and guidance to the Regional Hubs in the producing and distributing the Open DNA Collections/toolkits to the Hubs for redistribution. Development of the toolkits will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines), which in turn helps to inform the potential users (startups and SMEs) in the UK biomanufacturing sector. |
| Collaborator Contribution | We partnered up with the Reclone Hub in Latin America - led by Prof María Teresa Damiani - to take the lead on this proposal and she was awarded $300,000 over two years (starting Feb-2025) to strengthen the Reclone Regional Hub in Argentina and establish new nodes in Chile and Peru. This aims to empower local labs with the tools and training to produce lab chemicals autonomously, enabling faster, cheaper, and more reliable research. The funding primarily supports researchers in Latin America to further develop the Open DNA Collections, which will be shared amongst all Hubs (in UK, Argentina, Ghana, and the Philippines) to enable research globally. For more information: https://www.science.org/content/article/scientists-latin-america-struggle-get-key-chemicals-and-other-reagents-experiments |
| Impact | Proposal only recently awarded and are in the early stages of sharing resources between UK and Argentina, and formalising plans for developing and subsequently sharing the updated Open DNA Collections. |
| Start Year | 2024 |
| Title | OpenPlant Automation Protocols Github Repository |
| Description | The Open Bioeconomy Lab and the Earlham Institute are collaborating to validate and make available a library of protocols and automation scripts for the Opentrons OT2 platform via github. We hope this collection of protocols can inspire more researchers to adapt their workflows for automation, enabling a higher throughput and efficiency in general molecular biology work. The current protocols cover minipreps using magnetic beads and custom labware design files. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Only released in 2023 and will be updated throughout the year, no notable impacts expected yet. |
| URL | https://github.com/openplant/openplant_automation_protocols |
| Description | OECD Global Technology Forum Synthetic Biology Expert Group |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Jenny Molloy contributed to the work of the OECD Global Technology Forum Synthetic Biology Expert Group, including presenting to the group on access, equity and open source in synthetic biology. The work of the group led to the OECD report: Synthetic biology in focus: Policy issues and opportunities in engineering life, published in 2025. Dr Molloy also participated in the Hoover-OECD workshop "Pathways to Responsible Innovation and Anticipatory Governance of Synthetic Biology" on Thursday, 27 February, 2025 which aimed to further plan the policy implications and recommendations related to the issues raised in the report. |
| Year(s) Of Engagement Activity | 2023,2024,2025 |
| URL | https://www.oecd.org/en/blogs/2025/02/synthetic-biology-a-game-changer-for-economic-sustainability-s... |
| Description | Reclone Community Meetings (monthly) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Through the Reclone Initiative, we aim to build out a wider international community of researchers, with a focus on openly sharing knowledge and resources around existing open-source and OpenPlant-funded DNA collections as blueprints for future communities that would use the toolkit emerging from this project. Since the initiative began in December-2022, up to 30 international researchers have attended each session of our online series of monthly community meetings (https://reclone.org/meetings/), and where we have heard from 23 researchers who have used and/or developed upon the Open DNA Collections (stewarded by the Reclone Community) for low-cost diagnostics, reagent and hardware manufacturing. The March-2023 meeting saw community members discuss new DNA parts to add to these DNA collections (https://stanford.freegenes.org/collections/open-genes). A shortlist of these suggested parts were subsequently synthesised, and are in the workflow to be included in future to phase 2 of the Open DNA Collection. Phase 1 of the collection parts have already been distributed to at least three institutes in Latin America, Africa, and Asia, who are acting as regional reagent distribution hubs for other local researchers, and who are in a position to more easily make use of and re-distribute these collections. The collections have also been distributed to a number of research groups (academic and commercial entities) within the UK. We will continue sharing current updates of how researchers are using these collections for their own research through the monthly Reclone Community Meetings. |
| Year(s) Of Engagement Activity | 2022,2023,2024,2025 |
| URL | https://www.youtube.com/@reclone_org |
| Description | Science News article on Reclone Latin America |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article as part of Science "Global equity in Science" editorial series highlighting Reclone Latin American network to take forward distribution and development of open DNA collections for local manufacturing of reagents. Led to >5 connections to new collaborators, discussions and funding proposals ongoing. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.science.org/content/article/scientists-latin-america-struggle-get-key-chemicals-and-othe... |