Software Environment for Actionable & VVUQ-evaluated Exascale Applications (SEAVEA)
Lead Research Organisation:
Brunel University London
Department Name: Computer Science
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
Bhati AP
(2023)
Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets.
in Journal of chemical theory and computation
Bhati AP
(2025)
Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.
in Journal of chemical theory and computation
Freek B
(2024)
Analysing the effect of a dynamic physical environment network on the travel dynamics of forcibly displaced persons in Mali
in International Journal of Network Dynamics and Intelligence
Groen D
(2023)
FabSim3: An automation toolkit for verified simulations using high performance computing
in Computer Physics Communications
Groen D
(2023)
Facilitating simulation development for global challenge response and anticipation in a timely way
in Journal of Computational Science
Lo SCY
(2024)
Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations.
in Journal of the Royal Society, Interface
| Description | We found that the SEAVEA toolkit is capable to be used widely in the UK, across application domains. The use of surrogate models has delivered promising results in many areas, but training these models is highly problem-specific and not always straightforward. We also discovered that the SEAVEA toolkit has great reuse potential for ML/AI approaches, as the UQ performed on those algorithms is highly primitive, and these algorithms in particular suffer from issues in terms of robustness and explainability. In technical terms, we also discovered that multi-factor authentication can be combined with automation tools to enable users to create and use automation tools in a secure and convenient way, greatly widening the uptake of our toolkit. |
| Exploitation Route | SEAVEAtk is free to use by anybody and has in fact already been adopted in several other UK projects (e.g. in fusion), as well as in a EU-funded project (HOMEPOT, project number to emerge soon) and a UNHCR-funded project. |
| Sectors | Digital/Communication/Information Technologies (including Software) Energy Environment Pharmaceuticals and Medical Biotechnology Security and Diplomacy Other |
| URL | https://www.seavea-project.org |
| Description | Our VVUQ activities in the field of migration have led to official collaborations with three major NGOs: UNHCR, Save the Children and Open Doors International. The ensemble forecasting and validation approaches provided in SEAVEAtk are central to providing the credibility needed for Flee to be usable in an operational settings. |
| First Year Of Impact | 2022 |
| Sector | Government, Democracy and Justice,Security and Diplomacy,Other |
| Impact Types | Societal Policy & public services |
| Description | Fine Tuning Of The Model |
| Amount | € 254,563 (EUR) |
| Funding ID | RBE_001_2025 |
| Organisation | United Nations (UN) |
| Department | United Nations High Commissioner for Refugees |
| Sector | Public |
| Country | Switzerland |
| Start | 03/2025 |
| End | 12/2025 |
| Title | EasySurrogate |
| Description | EasySurrogate facilitates the creation of surrogate models. These models are simplified representations of complex simulations, allowing for faster evaluation of results. This is useful for tasks like optimisation or uncertainty quantification, where many simulation runs are needed. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | See papers. |
| URL | https://github.com/wedeling/EasySurrogate |
| Title | EasyVVUQ |
| Description | This tool is for Verification, Validation, and Uncertainty Quantification (VVUQ). It provides a framework for analysing the reliability of simulations by assessing uncertainties in input parameters and validating simulation results against experimental data. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | EasyVVUQ has been used to strengthen SEAVEA applications by enabling robust uncertainty quantification and validation, building confidence in simulation results and facilitating model improvement. |
| URL | https://github.com/UCL-CCS/EasyVVUQ |
| Title | FabSim3 |
| Description | FabSim3 is an automation toolkit for computational research. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | See paper. |
| URL | https://fabsim3.readthedocs.io |
| Title | MOGP Emulator |
| Description | MOGP (Multi-Output Gaussian Process) Emulator is a tool that builds statistical emulators, or surrogate models, that can handle multiple outputs from a simulation. This is particularly valuable when simulations produce a range of results that need to be analysed. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | See papers. |
| URL | https://github.com/alan-turing-institute/mogp-emulator |
| Title | MUSCLE3 |
| Description | Muscle3 is focused on enabling the coupling of multiscale simulations. This means it helps connect different simulation models that operate at different levels of detail (e.g., atomic-level and macroscopic). It's used for simulations that represent complex systems with interactions across different scales. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | See papers. |
| URL | https://github.com/multiscale/muscle3 |
| Title | QCG PilotJob |
| Description | QCG PilotJob is used for executing application workflows on HPC resources. It provides a way to manage and schedule complex jobs, making it easier to run simulations that involve multiple steps or components. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | See papers. |
| URL | https://github.com/psnc-qcg/QCG-PilotJob |
| Title | RADICAL-Cybertools |
| Description | RADICAL-Cybertools is a set of tools designed to enable the execution of large-scale, data-intensive applications on distributed computing resources. It provides abstractions and tools to manage the complexity of running such applications on cyberinfrastructure. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | See papers. |
| URL | https://radical-cybertools.github.io |
| Description | Partnership with Columbia University |
| Organisation | Columbia University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We provide support on executing ensemble models and provide support on the Flee modelling code. |
| Collaborator Contribution | They lead the applied research projects, and provide support on optimisation and model enhancement. |
| Impact | https://ui.adsabs.harvard.edu/abs/2023AGUFMGC31I1143P/abstract https://ui.adsabs.harvard.edu/abs/2022AGUFMGC35I0801P/abstract |
| Start Year | 2023 |
| Description | Partnership with ISI Kolkata |
| Organisation | Indian Statistical Institute (ISI) |
| Country | India |
| Sector | Academic/University |
| PI Contribution | Submitted a paper on Sensitivity Analysis in collaboration with ISI Kolkata. |
| Collaborator Contribution | Provided expertise on the SEAVEA toolkit |
| Impact | Submitted paper on Sensitivity Analysis |
| Start Year | 2022 |
| Description | Partnership with Save the Children in developing Flee 3.0 |
| Organisation | Save the Children UK |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We are incorporating a range of features into the Flee code and the associated FabFlee plugin, and are performing sensitivity analysis using the tools. |
| Collaborator Contribution | They test out the Flee code on a realistic setting, perform pre- and post-processing, and inform our assumptions. |
| Impact | This is a multi-disciplinary collaboration between computer science and the humanitarian sector. Several internal reports have been published so far. |
| Start Year | 2021 |
| Description | Partnership with World Watch Research |
| Organisation | Open Doors |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | We are developing a migration model of Nigeria for validation and to help understand the situation there. |
| Collaborator Contribution | They have provided funding and access to relevant data. |
| Impact | Outputs in progress. |
| Start Year | 2024 |
| Title | FabSim3 v3.6 |
| Description | FabSim3 is a Python-based automation toolkit for scientific simulation and data processing workflows, licensed under the BSD 3-clause license. Among other things, FabSim3 supports the use of simple one-liner commands to: Enable execution of simulation and analysis tasks on supercomputers. Establish and run coupled models using the workflow automation functionalities. Organize input, output and environment information, creating a consistent log and making it possible by default to repeat/reproduce runs. Perform large ensemble simulations (or replicated ones) using a one-liner command. Users can perform complex remote tasks from a local command-line, and run single jobs, ensembles of multiple jobs, and dynamic workflows through schedulers such as SLURM, PBSPro, LoadLeveller and QCG. FabSim3 stores machine-specific configurations in the repository, and applies it to all applications run on that machine. These configurations are updated by any contributor who feels that a fix or improvement is required. |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | FabSim3 is in use across a range of EU and UK research projects. |
| URL | https://fabsim3.readthedocs.io/en/latest/ |
| Title | Flu And Coronavirus Simulator v2.0.0 |
| Description | FACS is an agent-based modelling code that models the spread of flu and coronaviruses in local regions. Up to now, we have used it to model the spread of Covid-19 in a range of London boroughs. The code can be repurposed to model other regions, and its current (sequential) implementation should be able to run up to 500,000 households within a reasonable time frame. It also supports vaccination programmes, track and trace and mutated versions of the virus. What sets FACS apart from many other codes is that we have a partially automated location extraction approach from OpenStreetMaps data (the scripts reside at https://www.github.com/djgroen/covid19-preprocess), that we resolve a wide range of different location types (e.g., supermarkets, offices, parks, schools, leisure locations and hospitals) and that we have a specific algorithm for modeling infections within these locations, taking into account the physical size of each location. V2.0.0 is the first version that supports parallel execution using MPI. |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | FACS is in use across several trials in the EU-funded STAMINA project. |
| URL | https://facs.readthedocs.io |
| Title | wedeling/EasyVVUQ: Covidsim version |
| Description | Version of EasyVVUQ used to generate the results of: W. Edeling. H. Arabnejad, R. Sinclair et al, The Impact of Uncertainty on Predictions of the CovidSim Epidemiological Code, Nat Comp Sci, 2021. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Impact | This version was used to provide a VVUQ analysis of the CovidSim modelling code, which was directly used to inform UK policy decision making during the pandemic. |
| URL | https://zenodo.org/record/4445140 |
| Description | ABM Workshop - Glasgow |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | At an Exampler project workshop, we presented the SEAVEA toolkit, connecting agent-based modelling expertise from Exampler with the SEAVEAtk. |
| Year(s) Of Engagement Activity | 2024 |
| Description | CIUK ExCALIBUR session at Manchester Central, Manchester, UK |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We supported the ExCALIBUR activities at this event and presented the SEAVEA toolkit during two days of the conference. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.scd.stfc.ac.uk/Pages/CIUK2023.aspx |
| Description | CompBioMed & SEAVEA workshop at Science Congress Center Munich, Garching, Germany |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We gave a tutorial about the SEAVEA toolkit and organised a discussion workshop at this event. We also organised a Hackathon. |
| Year(s) Of Engagement Activity | 2023 |
| Description | ExCALIBUR Workshop on Exascale Computing co-located with ICCS 2024 - Malaga, Spain |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The ExCALIBUR Workshop on Exascale Computing, held in conjunction with the 24th International Conference on Computational Science (ICCS 2024) on July 1, 2024, served as a platform for ExCALIBUR project researchers to showcase their latest advancements and foster collaboration. Participants from PAX-HPC, SEAVEA, CompBioMedX, CompBioMedEE, QEVEC, EXA-UQ, and EXAMPLER shared insights into their work, covering a diverse range of applications from simulating human anatomy to developing real-time policy evaluation tools. The workshop featured a mix of presentations and panel discussions, receiving positive feedback from attendees. With an audience of approximately 15-30 individuals primarily from ExCALIBUR projects and ICCS 2024, the event provided a valuable opportunity for networking and knowledge exchange within the exascale computing community. |
| Year(s) Of Engagement Activity | 2024 |
| Description | HiDALGO, CIRCE & SEAVEA workshop - Stuttgart, Germany |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented the SEAVEA toolkit and provided hands-on tutorials and assistance for new users. |
| Year(s) Of Engagement Activity | 2024 |
| Description | HiDALGO, CIRCE & SEAVEA workshop on Uncertainty Quantification |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A collaborative workshop where we exchanged expertise in ensemble forecasting, validation and uncertainty quantification in the global challenges domain. This online event also kicked off the planning of an in person workshop in 2024. |
| Year(s) Of Engagement Activity | 2023 |
| Description | ICCS SEAVEA Workshop titled 'VVUQ on the Exascale' at Brunel University London |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | We organised a discussion workshop VVUQ on the exascale, in which we discussed the best strategic directions of development and outreach for the SEAVEA project, identifying gaps and opportunities. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.iccs-meeting.org/iccs2022/ |
| Description | Online SEAVEA Hackathon using Dorahacks |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This Hackathon event led to the development of new applications, as well as a new library for the SEAVEA toolkit. It also sparked questions and project ideas among a wider audience. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://dorahacks.io/hackathon/seavea |
| Description | SEAVEA Hackathons |
| 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 | We have delivered five Hackathon events: ICCS SEAVEA Hackathon (24 June 2022) at Brunel University London [Derek, Diana, Yani, Maziar and Alireza] SEAVEA Hacakthon at University College London (8-9 December 2022) [Derek, Diana, Arindam, Yani and Alireza] SEAVEA Hackathon at Brunel University London (26-27 June 2023) [Derek, Diana, Maziar, Yani, Alireza, Arindam, Maziar and Rumyana] CompBioMed & SEAVEA Hackathon at LRZ, Garching, Germany (15 September 2023) [Diana] SEAVEA Hacakthon at University College London (1, 4-5 December 2023) [Derek, Diana, Maziar, Yani, Alireza, Laura and Rumyana] |
| Year(s) Of Engagement Activity | 2021,2022,2023,2024 |
| URL | https://www.seavea-project.org/news-events/ |
| Description | SEAVEA knowledge exchange at HPC for ABMs Workshop, Aberdeen, UK |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop organised by the Exampler project. We presented the SEAVEA toolkit and provided tutorial content to support people in using SEAVEAtk and HPC in general. This has linked up the Agent-based modelling expertise in SEAVEA with that in the Exampler project. |
| Year(s) Of Engagement Activity | 2024 |
| Description | SEAVEA knowledge exchange workshop at Leogang, Austria |
| 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 | This was a discussion workshop about VVUQ, AI, Visualisation and HPC. It led to some essential insights in how the SEAVEA toolkit can be applied to resolve long-standing issues in the trustworthiness and reliability of ML algorithms. In addition, we made several groups aware internationally of the SEAVEA toolkit and identified several new research collaborations for members in our group. |
| Year(s) Of Engagement Activity | 2024 |
| Description | SEAVEA workshop at Physics and Applied Mathematics Unit in Indian Statistical Institute Kolkata |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A SEAVEA workshop where we organised a hackathon and a tutorial for the SEAVEA toolkit at ISI Kolkata. Led to a partnership with them. |
| Year(s) Of Engagement Activity | 2022 |