Business Case for a Catalyst Partnership in Artificial Intelligence between the Alan Turing Institute and the Norwich Biosciences Institutes
Lead Research Organisation:
Earlham Institute
Department Name: Directorate Office
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Publications
Rees H
(2022)
Circadian regulation of the transcriptome in a complex polyploid crop.
in PLoS biology
| Description | Following the successful recruitment each fellow started their individual projects: 1. Predicting Plant Immunity Triggering Protein Interactions From Sequence Data ( TSL) 2. Estimation of gene-gene regulatory networks with recurrent neural networks and meta-learning (EI) 3. Uncovering the cis-regulatory patterns that determine gene expression (EI) 4. In too Deep: Unravelling the links between transcriptome dynamics and phenotypic changes in Brassicas using deep learning, (JIC). 5. Predicting the phase of the endogenous circadian clock in plants (EI/JIC) 6. Machine learning for phenotypic trait inference from microbial genomes (EI/QIBI). We have encouraged interactions between the fellows and the projects from the outset. To promote such interactions and communication, the fellows meet once every two weeks for a joint journal club in which all fellows read a selected journal publication and one fellow presents it in detail to the others, followed by questions, discussion, critical assessment and how the finding may be applicable to their projects. Topics of these discussions have included programming languages, AI frameworks and tools, and github. Several 1:1 meetings between the fellows have followed as a result of these meetings. Once a month, we have an informal cohort meeting, chaired by Richard Morris (John Innes Centre). Each meeting consists of an update from all fellows, two detailed progress presentations, followed by a discussion and problem solving session. Sebastian Ahnert (the Alan Turing Institute ATI) is in attendance at these meetings and offers mentoring, guidance, and suggestions for ATI courses/workshops. Several fellows have jointly attended AI workshops run by ATI. One fellow took on the supervision of an undergraduate for an eight week summer project and got them enthused about AI for automated phenotyping. It is clear that the cohort activities are working well (more so than expected given the circumstances with remote working during this period) and in this regard has already proven to be a key aspect of this programme. Following the success of the initial stages of this programme BBSRC have awarded further funding to provide an extension of the programme up until the end of September 2022. In February 2022 on the anniversary of the first fellows starting the programme, all the fellows took part in a "Showcase" virtual event to present their projects to the Norwich Research Park. Following this event in July 2022 an in-person symposium was held in the John Innes Conference Centre to celebrate their work, attendees included those external to the Norwich Research Park. |
| Exploitation Route | As a measure of the success of this programme five out of the six fellows completed the programme in September 2022 to successful step into new relevant roles. Three have remained within academia: two of which are still at the Norwich Research Park and the other taking on a machine learning role with another University. Whilst, another two of the fellows have gone on to external research related industrial facing positions. Besides the clear focus of this programme on the individual fellows the objectives of this programme were also to increase engagement with industry and the Turing. Within EI we have had a number of successes in this regard and these are highlighted in the narrative impact. |
| Sectors | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Other |
| Description | Besides the clear focus of this programme on the individual Turing fellows the objectives of this programme were also to increase engagement with industry and the Turing. Within EI we have had a number of successes in this regard. Professor Anthony Hall's group has been able to foster existing relationships with IBM Research working on AM/ML based projects and together they have secured a NRPDTP Case Studentship to start October 2023. Dr. Wilfried Haerty (EI) has been working with Turing Fellow Dr. Sebastian Ahnert to include his expertise in machine learning and regulatory network reconstruction in EI's future Institute Strategic Programme "Cellular Genomics" (scheduled to begin in April 2023), with Dr Ahnert included as a Co-Investigator, and contributing to a number of work packages and deliverables. As part of the proposed strategic programme, a postdoctoral research scientist will be working with Dr Ahnert at the Turing. Professor Anthony Hall is leading a multi-centre application for a Centre for Doctoral Training in Artificial Intelligence: UKRI AI Centre for Doctoral TRaining in Agri-food INnovation (TRAIN). This will train 66 students across nine institutions and two industrial partners over eight years. UKRI funding in excess of £8million has been requested for 60 students, with a further six students funded by the institutions. An outline application has been submitted (February 2023). |
| First Year Of Impact | 2023 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software) |
| Impact Types | Economic |
| Description | BBSRC NRPDTP Studentship - Using machine learning to tell the time |
| Amount | £100,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2022 |
| End | 09/2026 |
| Description | Canada Partnering Award |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2022 |
| Description | Further Funding Business Case for a Catalyst Partnership in Artificial Intelligence between the Alan Turing Institute and the Norwich Biosciences Institutes |
| Amount | £300,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2021 |
| End | 09/2022 |
| Description | The Horticultural Quality and Food Loss Network - Networking Visit Fund |
| Amount | £2,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2022 |
| Description | Catalyst Partnership in AI across the Norwich Bioscience Institutes. |
| Organisation | John Innes Centre |
| Department | The Sainsbury Laboratory |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | There are project supervisors based at all the Norwich Bioscience Institutes partners listed - these project supervisors will manage the fellows and ensure that they work together as a cohort between the Norwich Bioscience Institutes. |
| Collaborator Contribution | Each partner has been involved with project proposal submission, project review and recruitment of the fellows. As the fellows are only just beginning the programme, each partner will work with them to ensure the fellows work as a cohort. |
| Impact | This project ended recently in September 2022 - outcomes and outputs are still being formulated |
| Start Year | 2020 |
| Description | Catalyst Partnership in AI across the Norwich Bioscience Institutes. |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | There are project supervisors based at all the Norwich Bioscience Institutes partners listed - these project supervisors will manage the fellows and ensure that they work together as a cohort between the Norwich Bioscience Institutes. |
| Collaborator Contribution | Each partner has been involved with project proposal submission, project review and recruitment of the fellows. As the fellows are only just beginning the programme, each partner will work with them to ensure the fellows work as a cohort. |
| Impact | This project ended recently in September 2022 - outcomes and outputs are still being formulated |
| Start Year | 2020 |
| Description | Catalyst Partnership in AI across the Norwich Bioscience Institutes. |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | There are project supervisors based at all the Norwich Bioscience Institutes partners listed - these project supervisors will manage the fellows and ensure that they work together as a cohort between the Norwich Bioscience Institutes. |
| Collaborator Contribution | Each partner has been involved with project proposal submission, project review and recruitment of the fellows. As the fellows are only just beginning the programme, each partner will work with them to ensure the fellows work as a cohort. |
| Impact | This project ended recently in September 2022 - outcomes and outputs are still being formulated |
| Start Year | 2020 |
| Description | Collaboration on AI for bioscience with the Alan Turing Institute |
| Organisation | Alan Turing Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Our team have identified areas of Bioscience research that can be investigated using AI techniques. We have hired fellows supported by this award that will have 12 months training in AI from our collaborative partner |
| Collaborator Contribution | Advice and mentorship in the application of AI. A training programme is to be provided to the hired fellows. |
| Impact | This is a very new award |
| Start Year | 2020 |
| Title | GAGA: a pipeline for GEM And GWAS Automation |
| Description | The GAGA pipeline is an R package for GWAS And GEM Automisation. The pipeline has been designed to provide a user-friendly method of analysing multiple traits using both GEM and GWAS analysis automatically in hours. GAGA relies on the pre-existing GAPIT3 package1 to complete the GWAS analysis. |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Still very new, it has been trialled by partners at National Plant Phenomics Centre |
| Description | ATI Fellows presented their projects to the Norwich Research Park |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | A virtual showcase event to present all six ATI Fellow's and their projects to the Norwich Research Park. |
| Year(s) Of Engagement Activity | 2022 |
| Description | ATI - Norwich Bioscience Institute Fellows Symposium - July 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | A in-person showcase event to present all six ATI Fellow's and their projects to the Norwich Research Park. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Alan Turing Institute and Norwich Bioscience Institute Fellows Symposium |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | An in-person showcase event to present all six ATI Fellow's and their projects to the Norwich Research Park partners. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Fellow attended and presented poster at European Biological Rhythms Society 2022 Zurich |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Fellow attended the European Biological Rhythms Society 2022 conference in Zurich, where they presented a poster showing their results for ChronoGauge, also attended an early career research training event at said conference. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.ebrs2022.uzh.ch/en/Posters/P1.html |
| Description | Fellow presented a talk at the Society of Experimental Biology 2021 Annual Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | One of the Fellows presented their talk at the Plant Phenotyping Session. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://eu.eventscloud.com/website/4875/agenda/ |
| Description | Fellow presented a talk at the Norwich Science Festival 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | One of the ATI Fellows presented a talk at the Norwich Science Festival on "Revolutionising agricultural science". |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://norwichsciencefestival.co.uk/whats-on/agrificial-intelligence-2021 |
| Description | Norwich Bioscience Institute and Alan Turing Institute workshop - September 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Our Norwich Bioscience Institute - Turing fellows met with a number of Turing members at the Alan Turing Institute offices at the British Library. Attendees at this event included Turing fellows, other members of John Innes Centre, Science and Technology Facilities Council and Rothamsted Research. This workshop consisted of short talks from all attendees and opportunities to discuss current and future collaborations. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Talks from ATI Fellows at the Earlham Institute Innovate Event 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Earlham Institute Innovate 2021: Linking datasets and bioscience online event 17 November 2021: Four of our Fellows presented their projects to demonstrate applications of machine learning/artificial intelligence to biological research datasets across the Norwich Research Park, their talks took place directly before the Q&A discussion panel session. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/ei-innovate-2021-linking-datasets-and-bioscience#Programme-2 |