The Earlham Institute 2021 Flexible Talent Mobility Account
Lead Research Organisation:
Earlham Institute
Department Name: Directorate Office
Abstract
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People |
ORCID iD |
| Neil Hall (Principal Investigator) |
| Description | Introductory videos will be shared with potential collaborators to best identify and assess suitability of the BioFoundry equipment for their desired research. This will also impact the BioFoundry staff by way of reducing the amount of time required on-site for visitors once a collaborative project is underway by way of offering introductory material for individuals to explore at their leisure - has increased capacity for commercial users of the foundry Developed experience in the operation of the Biolector and Robolector instrumentation and software, some troubleshooting capability for both and significant development of know-how to maximise the efficiency of Biolector experiements through experimental design - has benefited commercial users of the foundry Improved understanding of the principles of designing robust bioinformatic pipelines for workflow and containerisation and delivery; Introduction to cloud-based models; Introduction to web-based user-interface development and design - has enabled collaboration with industry Through the skills developed, discussions and ad hoc troubleshooting the individuals have substantially increased their knowledge and confidence in setting up microfluidics devices. Following the visit, the trainees can now optimise and thoroughly validate the approach, obtaining preliminary data which will be used to support grant applications. It is anticipated that at least one of the trainees will apply for a joint application for PhD studentship co-funded by the BHF and/or Wellcome grants (Discovery Award or Technology Development) - this has also led to a collaboration with two microfluidics companies |
| First Year Of Impact | 2022 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Electronics,Healthcare,Manufacturing, including Industrial Biotechology |
| Impact Types | Economic |
| Description | Exploring the application of pangenomic approaches to plant breeding |
| Organisation | IBM |
| Department | IBM Research in the UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration, I was (virtually) seconded to IBM Research for 3 months. During this time I developed and adapted workflows implementing existing pangenome graph building tools and tested these in different plant species. |
| Collaborator Contribution | As part of this collaboration IBM shared their expertise of designing and scaling bioinformatic workflows and how these would be transformed into user friendly platforms hosted in a hybrid cloud environment. RAGT shared specific domain knowledge that ensured the collaboration delivered novel results that would add insight into their plant breeding programme. The University of Tennessee provided software development expertise and intellectual input that enabled us to understand, adapt and test existing pangraph building tools. |
| Impact | This collaboration now forms part of an ongoing IBM Research Excelerate project between EI, IBM and RAGT. It has also led to the development of a new project, recently submitted to the BBSRC-NSF funding call; BB/Y000935/1 '2022BBSRC-NSF/BIO-Building foundational pangenome tools and infrastructures to address an unmet need in fundamental plant science and crop breeding'. I attended the Computational Pangenomics course at Instituto Gulbenkian de Ciência (IGC) - Oeiras, Portugal in May 2022 to study methods to build and interrogate pangenome graphs. |
| Start Year | 2022 |
| Description | Exploring the application of pangenomic approaches to plant breeding |
| Organisation | RAGT Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration, I was (virtually) seconded to IBM Research for 3 months. During this time I developed and adapted workflows implementing existing pangenome graph building tools and tested these in different plant species. |
| Collaborator Contribution | As part of this collaboration IBM shared their expertise of designing and scaling bioinformatic workflows and how these would be transformed into user friendly platforms hosted in a hybrid cloud environment. RAGT shared specific domain knowledge that ensured the collaboration delivered novel results that would add insight into their plant breeding programme. The University of Tennessee provided software development expertise and intellectual input that enabled us to understand, adapt and test existing pangraph building tools. |
| Impact | This collaboration now forms part of an ongoing IBM Research Excelerate project between EI, IBM and RAGT. It has also led to the development of a new project, recently submitted to the BBSRC-NSF funding call; BB/Y000935/1 '2022BBSRC-NSF/BIO-Building foundational pangenome tools and infrastructures to address an unmet need in fundamental plant science and crop breeding'. I attended the Computational Pangenomics course at Instituto Gulbenkian de Ciência (IGC) - Oeiras, Portugal in May 2022 to study methods to build and interrogate pangenome graphs. |
| Start Year | 2022 |
| Description | Exploring the application of pangenomic approaches to plant breeding |
| Organisation | University of Tennessee Health Science Center |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | As part of this collaboration, I was (virtually) seconded to IBM Research for 3 months. During this time I developed and adapted workflows implementing existing pangenome graph building tools and tested these in different plant species. |
| Collaborator Contribution | As part of this collaboration IBM shared their expertise of designing and scaling bioinformatic workflows and how these would be transformed into user friendly platforms hosted in a hybrid cloud environment. RAGT shared specific domain knowledge that ensured the collaboration delivered novel results that would add insight into their plant breeding programme. The University of Tennessee provided software development expertise and intellectual input that enabled us to understand, adapt and test existing pangraph building tools. |
| Impact | This collaboration now forms part of an ongoing IBM Research Excelerate project between EI, IBM and RAGT. It has also led to the development of a new project, recently submitted to the BBSRC-NSF funding call; BB/Y000935/1 '2022BBSRC-NSF/BIO-Building foundational pangenome tools and infrastructures to address an unmet need in fundamental plant science and crop breeding'. I attended the Computational Pangenomics course at Instituto Gulbenkian de Ciência (IGC) - Oeiras, Portugal in May 2022 to study methods to build and interrogate pangenome graphs. |
| Start Year | 2022 |
| Description | Wild beet host-pathogen genomic surveillance |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | Knowledge exchange to summarise our advances in using wild beet pathogen (rust) genomic diversity to identify virulence important for pathogen success on the sugar beet crop. We also outlined our wild beet sequencing project in which, in collaboration with KWS, we have sequenced hundreds of wild beets and are assembling wild beet genomes. Our aims there are to identify novel resistance genes. |
| Collaborator Contribution | Our partners summarised their work on numerous sugar beet and pathogen work streams. We focussed primarily on their cercospora work which we identified was a key area for collaboration. This related to USDA expertise in pathogen wild and wet lab biology, their culture collection and understanding of the population genomics and pathology on sugar beet in the USA. |
| Impact | This collaboration has resulted in a proof of concept experimental proposal being submitted (and taken on) for the one year Earlham Institute Year in Industry program. Promising early results have inspired talks for funding a two year PDRA. |
| Start Year | 2022 |
| Description | Career development workshop and networking with Eagle Genomics |
| 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 | Postgraduate students |
| Results and Impact | The objective of this interaction with Eagle Genomics is to support mobility of researchers at the Earlham Institute, support the skills development among early career researchers, and explore opportunities for longer term collaborations. The objective is to facilitate a travel of 2 members of Eagle Genomics to the Earlham Institute. The aims of the visit are: 1) to increase an understanding among ECRs of how to work with in industry and build transferable skills relevant to the data driven, cross-disciplinary bioinformatic workforce and to improve employability of ECRs. 2) To facilitate 1:1 and group meetings between Earlham researchers and Eagle colleagues to improve engagement and interaction, and to explore opportunities for longer term collaborations. These were the specific skills development learning objectives of this activity: 1. Gain Insight of career paths and life in industry 2. Learn how to engage with industry 3. Gain transferable skills that could be useful for transition into industry, and how to build on existing skills gaps 4. To discuss areas of potential future collaborative work. We hosted a workshop on career and skills development for early career researchers. The target audience will be PhD students who are interested in understanding what skills are the required skills to improve employability, and postdoctoral researchers who are interested to collaborate with Eagle Genomics. The second activity will be 1:1 and group meetings with researchers, to discuss the wider activity taking place at EI and Eagle, and discuss bespoke areas of complementary interests for new and existing collaborations in more detail, and build strategic partnerships. The target audience for this were PIs and postdocs. Building upon previous virtual visits, the in-person element of this visit helped build personal connections and rapport to strengthen this strategic partnership, identify tangible areas of collaboration/ interactions, as well as the appropriate routes to do so. The networking lunch with Eagle colleagues helped ECRs to practice their networking and interpersonal skills for their professional and personal development and improve their employability. There was also a networking dinner between Eagle and EI's senior researchers/ group leaders, to enable them to connect on a personal level in an informal setting. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Earlham Institute's Flexible Talent Mobility Account Award, 3 day bespok workshop at Earlham Institute |
| 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 | Professional Practitioners |
| Results and Impact | Supported by Earlham Institute's Flexible Talent Mobility Account Award (BB/W510890/1) we hosted a visitor (JJW) from University of Southampton for a 3 day workshop for myself and one other participant (MB). Skills: 1.obtaining stable droplet with beads 2. obtaining droplets with a megakaryocyte and a bead 3. generating libraries from emulsion Skills developed during the workshop with Dr. West will help me facilitate my own research. Through discussions and ad hoc troubleshooting, I have gained more confidence in setting up the microfluidic device. I have realised which further improvements I can implement to further optimise the current set up. After implementing them I will perform library construction of captured cells. Importantly, we have obtained high rate of 1 in 7 cells being conecapsulated with the bead. Through discussion with Dr West we can further increase it applying Dean entrainment system to reach coencapsulation rate of 1 in 2 cells. After implementing these modifications, I will pursue library construction using generated emulsion. This was an extension of a previus workshop (February 2022), which facilitated the generation of preliminary data for new funding options including: 1. Joint application for a PhD student funded or co-funded by British Heart Foundation 2. BBSRC standard research grant I intend to apply for Wellcome Career Development Award (call September 2022) including preliminary data generated during this workshop. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Guest Lecture Cornell |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to give a guest lecture at Cornell University after a visit. The lecture was on the population genetics of fungal invasions with reference to the ash dieback pathogen and crop pathogen emergence. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited talk -Crop pathogen invasion and adaptation |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An invited talk with USDA Fargo beet researchers to consider the population genetics signals associated with crop pathogen invasion and adaptation. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Production of 3 Earlham Institute Biofoundry training videos supported by the Award BB/W510890/1 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The activity consisted of the preparation of 3 training videos produced with EyeFilm. The purpose of these videos (Opentrons, Echo and Biolector) is to introduce 3 pieces of the equipment and protocols used in the Earlham Institute's Biofoundry, ahead of individuals arriving on site. The goal is that these videos will expedite the on-site training required while still providing these individuals with high-quality guidance and support. For each of the planned films, a script was developed and annotated with suggested shots or sections for animation/graphics. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://youtube.com/playlist?list=PL3lTC-_gPbd7zuGDqeAN0WdnD-KWxm0Ht |
| Description | Training at the Biofoundry supported by the Earlham Institute's Flexible Talent Mobility Account (FTMA) Award BB/W510890/1 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Industry/Business |
| Results and Impact | The activity consisted of the Earlham Institute Biofoundry staff providing training on the use of the Biolector and Robolector equipment. The trainee was CG from Colorifix. The purpose was to allow the trainee, CG from Colorifix staff to gain skills and be self-sufficient in both experimental design, software and hardware operation and analyses and interpretation of results. By exploiting the use of the Biolector and Robolector, Colorifix improved their throughput capability in screening strains and media, as well as increase the dataset generated from these experiments. This will serve to strengthen and fasten their pipelines when scaling-up processes to industrial fermentations. The trainee expressed that acquired the ability to confidently operate the Biolector and learning about the equipment additional uses and limitations, she will need support if troubleshooting is needed, which can be provided by EB staff. As impact, there are discussions ongoing about running more microfluidic experiments using the Biolector and likely Robolector with staff from Colorifix, there is an interest to explore using it for fed-batch fermentations. Impact/outcomes: There was a request about further involvement and running more microfluidics experiments at the Earlham Institute Biofoundry. |
| Year(s) Of Engagement Activity | 2022 |