Sustainable RSE Careers for Sustainable Software Development
Lead Research Organisation:
University of Bristol
Department Name: Faculty of Science
Abstract
Advances in High Performance Computing (HPC) and scientific software development will have increasingly significant societal impact through the computational design of new products, medicines, materials and industrial processes. However, the complexity of modern HPC hardware means that scientific software development now requires teams of scientists and programmers to work together, with different and non-overlapping skill-sets required from each member of the group. This complexity can lead to software development projects stalling. Investments in software development are in danger of being lost, either because key members of a team move on, or because a lack of planning or engagement means that a sustainable user and developer community has failed to gel around a particular code.
Research Software Engineers (RSEs) can solve this problem. RSEs have the skills and training necessary to support software development projects as they move through different stages of the academic software lifecycle. Academic software evolves along this lifecycle, from being a code used by an initial team of researchers, through to a large multi-site community code used by academics and industrialists from across the UK and around the World. RSEs provide the training and support needed to help academic software developers structure their projects to support the sustainable growth of their user and developer communities. RSEs are also highly skilled programmers who can train software developers in advanced HPC techniques, and who can support developers in the implementation, optimisation and testing of complex and intricate code. Together with academic software developers, RSEs can support UK investment in HPC, and ensure that the potential of computational science and engineering to revolutionise the design of future products and industrial processes is realised.
This project aims to develop sustainable RSE career pathways and funding at Bristol. This will support the growth of a sustainable team of RSEs at the University. Software development projects that will be supported include; the building of code to interface real biological cells with virtual simulated cells, so to support the rapid design of new biomanufacturing control processes; the development of code to more quickly model the behaviour of electrons in novel materials, to support the design of new fuel cells and batteries; code to improve our understanding of glass-like matter, so to help design new materials with exciting new properties; software to support modelling of the quantum interaction between laser light and microscopic nanoparticles, to support the design of optical tweezers and new optically driven nanomachines; and code to design new medicinal drugs and to understand why existing treatments are no longer working, thereby supporting the development of 21st century medicine.
Finally, this project aims to create a coherent set of teaching materials in programming and research software engineering. These, together with the development of software to support science and programming lessons held in an interactive 3D planetarium, will help inspire and educate the next generation of scientists and RSEs. These materials will showcase how maths, physics, computing and chemistry can be used in the "real world" to create the high-tech tools and industries of the future.
Research Software Engineers (RSEs) can solve this problem. RSEs have the skills and training necessary to support software development projects as they move through different stages of the academic software lifecycle. Academic software evolves along this lifecycle, from being a code used by an initial team of researchers, through to a large multi-site community code used by academics and industrialists from across the UK and around the World. RSEs provide the training and support needed to help academic software developers structure their projects to support the sustainable growth of their user and developer communities. RSEs are also highly skilled programmers who can train software developers in advanced HPC techniques, and who can support developers in the implementation, optimisation and testing of complex and intricate code. Together with academic software developers, RSEs can support UK investment in HPC, and ensure that the potential of computational science and engineering to revolutionise the design of future products and industrial processes is realised.
This project aims to develop sustainable RSE career pathways and funding at Bristol. This will support the growth of a sustainable team of RSEs at the University. Software development projects that will be supported include; the building of code to interface real biological cells with virtual simulated cells, so to support the rapid design of new biomanufacturing control processes; the development of code to more quickly model the behaviour of electrons in novel materials, to support the design of new fuel cells and batteries; code to improve our understanding of glass-like matter, so to help design new materials with exciting new properties; software to support modelling of the quantum interaction between laser light and microscopic nanoparticles, to support the design of optical tweezers and new optically driven nanomachines; and code to design new medicinal drugs and to understand why existing treatments are no longer working, thereby supporting the development of 21st century medicine.
Finally, this project aims to create a coherent set of teaching materials in programming and research software engineering. These, together with the development of software to support science and programming lessons held in an interactive 3D planetarium, will help inspire and educate the next generation of scientists and RSEs. These materials will showcase how maths, physics, computing and chemistry can be used in the "real world" to create the high-tech tools and industries of the future.
Planned Impact
The establishment of a sustainable career pathway, funding, and training of Research Software Engineers (RSEs) will directly impact all UK academics and industrialists whose research depends on the development of UK scientific code. The impact, sustainability and international reputation of UK academic software will be significantly enhanced by the sustainable growth of RSE teams, and a change in academic and funder culture to trust and support RSE involvement in academic software projects. This will maximise return on investment by the EPSRC in HPC and software development, and will multiply its impact by ensuring that outputs can be sustainably developed beyond the funded lifetimes of their projects. RSEs will help maximise this impact by embedding best practice in programming and sustainability into software development projects, and will support academic developers in creating robust, reusable, reliable, documented and fully-tested components that can be trusted and built-upon by future researchers.
This Fellowship will directly support the development of a sustainable RSE career pathway, and growth of an RSE team at Bristol. Significant impact will come from the large pool of researchers and RSEs who will benefit directly from the training and career development that will be provided. By working with and providing training that can be used by the CDTs, CCPs and Software Carpentry, I will help raise the knowledge-base of the UK software development community. The availability of a pool of trained and capable software developers and RSEs will encourage investment in software projects in the UK, consolidating the reputation of UK software on the international stage. This will directly benefit UK industry and academia, by supplying a steady flow of talented individuals with the programming, scientific and mathematical skills necessary to help the UK maintain its lead in the knowledge economy.
The scientific outputs supported by this Fellowship will have impact across a range of disciplines and industries. Software to be supported will have impact in areas such as biomanufacturing, catalyst design, novel materials, 21st century medicine and quantum technologies. The timescale for these impacts will depend on the progress of each piece of software along the academic software lifecycle. RSE support that understands this lifecycle can accelerate progress. This will ensure that the UK maintains its leading position in international research excellence, and has the software tools and trained personnel to encourage investment in future industry. Through collaboration with Cresset, a UK SME, I will develop pathways for rapid commercialisation of academic software, and a means by which academic software developers and RSEs can provide scientific consultancy. This will further enhance industrial impact, and provide a route by which EPSRC investment in software can show a demonstrable return to the UK economy.
Finally, I want to have impact by raising the public and academic profile of scientific software developers and RSEs. Through advertising successes of RSE projects at conferences, by providing publicly accessible training materials, and by creating interactive school science lessons in a 3D planetarium, this Fellowship aims to enthuse and inspire the next generation of students, scientists and software developers. I want to raise the profile of programming, physics, maths and chemistry, and show how they have real-world applications to help develop future technologies. I want to positively impact the career choices of students and young scientists by showing them that there is stable career pathway for scientific software developers and RSEs, that this is an exciting and dynamic career choice, it does let you work with intelligent and energetic people, it can allow you to travel around the World, and most importantly, it puts you in a position to shape how the technology of the future will be designed and developed.
This Fellowship will directly support the development of a sustainable RSE career pathway, and growth of an RSE team at Bristol. Significant impact will come from the large pool of researchers and RSEs who will benefit directly from the training and career development that will be provided. By working with and providing training that can be used by the CDTs, CCPs and Software Carpentry, I will help raise the knowledge-base of the UK software development community. The availability of a pool of trained and capable software developers and RSEs will encourage investment in software projects in the UK, consolidating the reputation of UK software on the international stage. This will directly benefit UK industry and academia, by supplying a steady flow of talented individuals with the programming, scientific and mathematical skills necessary to help the UK maintain its lead in the knowledge economy.
The scientific outputs supported by this Fellowship will have impact across a range of disciplines and industries. Software to be supported will have impact in areas such as biomanufacturing, catalyst design, novel materials, 21st century medicine and quantum technologies. The timescale for these impacts will depend on the progress of each piece of software along the academic software lifecycle. RSE support that understands this lifecycle can accelerate progress. This will ensure that the UK maintains its leading position in international research excellence, and has the software tools and trained personnel to encourage investment in future industry. Through collaboration with Cresset, a UK SME, I will develop pathways for rapid commercialisation of academic software, and a means by which academic software developers and RSEs can provide scientific consultancy. This will further enhance industrial impact, and provide a route by which EPSRC investment in software can show a demonstrable return to the UK economy.
Finally, I want to have impact by raising the public and academic profile of scientific software developers and RSEs. Through advertising successes of RSE projects at conferences, by providing publicly accessible training materials, and by creating interactive school science lessons in a 3D planetarium, this Fellowship aims to enthuse and inspire the next generation of students, scientists and software developers. I want to raise the profile of programming, physics, maths and chemistry, and show how they have real-world applications to help develop future technologies. I want to positively impact the career choices of students and young scientists by showing them that there is stable career pathway for scientific software developers and RSEs, that this is an exciting and dynamic career choice, it does let you work with intelligent and energetic people, it can allow you to travel around the World, and most importantly, it puts you in a position to shape how the technology of the future will be designed and developed.
People |
ORCID iD |
| Christopher Woods (Principal Investigator / Fellow) |
Publications
Dommer A
(2021)
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.
in bioRxiv : the preprint server for biology
Callegari D
(2018)
L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.
in Chemical science
Marucci L
(2020)
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology
in Frontiers in Bioengineering and Biotechnology
Gorman L
(2021)
What's Stopping Knowledge Synthesis? A Systematic Review of Recent Practices in Research on Smallholder Diversity
in Frontiers in Sustainable Food Systems
Abraham M
(2019)
Sharing Data from Molecular Simulations.
in Journal of chemical information and modeling
Haldar S
(2018)
A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics.
in Journal of chemical theory and computation
Raza S
(2019)
Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site.
in Journal of computer-aided molecular design
Hedges L
(2019)
BioSimSpace: An interoperable Python framework for biomolecular simulation
in Journal of Open Source Software
Woods C
(2022)
MetaWards: A flexible metapopulation framework for modelling disease spread
in Journal of Open Source Software
Oliveira ASF
(2019)
A General Mechanism for Signal Propagation in the Nicotinic Acetylcholine Receptor Family.
in Journal of the American Chemical Society
| Description | This award focussed on demonstrating that the individuals with software engineering skills had a role in academia. These individuals, called Research Software Engineers, sit between traditional researchers and professional software engineers. Such individuals, when this award was made, often had no home in academia. Their skills were not recognised and so they often left for industry. This meant that software engineering best practice was not retained in the academic sector, leading to low quality and poor sustainability of research software. The aim of the award was to help develop sustainable careers and funding pathways for research software engineering in academia. From this award I established the University of Bristol Research Software Engineering Group (@BristolRSE, https://bristol.ac.uk/acrc/research-software-engineering). I develop sustainable funding pathways at the University, such that now the group has 8 members, with two new positions in the process of being filled. Research Software Engineering is now established at Bristol as a key research enabling group. We developed a complete training curriculum that embeds core software engineering skills across the researcher community. We have about 2000+ attendances of our workshops each year. New grants from the University cost in time from a pool of RSEs. These RSEs have stable and fulfilling careers, being judged on metrics that relate to software engineering. The stability of their careers means that they have the confidence to buy houses and raise families. The quality of research software engineered at Bristol has significantly increased. Outside of Bristol, I worked with others to grow and develop the UK Association of Research Software Engineering into a full professional society, the Society of Research Software Engineering (https://society-rse.org). Through conferences, visiting Universities, working closely with funders etc I have helped move Research Software Engineering from being an idea, into now being an established and thriving community that is having a real impact on improving the quality of research software across the UK, and now internationally. The Society's Slack group has over 3000 members. Chapters of Research Software Engineering societies and Associations have now been created around the World (e.g. the USA, the Netherlands, Germany, Australia, https://society-rse.org/international-rse-organisations/). Research Software Engineering groups have been established at most of the research-intensive Universities in the UK, and RSEs are now included in funding applications, included as referees of papers and grants, and consulted by funders whenever there a project has an aspect of software engineering. We are now seeing case studies showing how Research Software Engineering is making a difference. We keep a set of case studies on our website (https://bristol.ac.uk/acrc/research-software-engineering/case-studies/). The most recent was a short project that involved a research software engineer accelerating a script that took 10 days to run, so that now it took just 34 seconds. This massively reduced the energy requirements for the script, while simultaneously opening up a whole new scale of analysis to the researcher (https://bristol.ac.uk/acrc/research-software-engineering/case-studies/minimalmarkers/#d.en.578273). The primary aim of the award, to establish a Research Software Engineering group has been successfully met. This is evidenced by me transitioning from a role as an EPSRC RSE Fellow to now being employed fully by the University as Head of Research Software Engineering. In this role, I can continue to grow and develop RSE at Bristol, continue to train researchers and embed software engineering good practice across the University, and can continue to work with the RSE community to improve the adoption and application of software engineering good practice by researchers across the UK. To quote the Software Sustainability Institute, Better Software, Better Research. |
| Exploitation Route | The outcomes of this funding are the demonstration that investment in Research Software Engineering improves the adoption of software engineering best practice by research groups, and thus improves the quality and sustainability of research software, leading to better research. These outcomes are being taken forward by working with Universities to establish RSE groups where they don't exist, and by working together with the wider RSE community to share best practice, training materials and skills. The ultimate aim is that research software engineering is universally recognised as an important component of a successful research university, and that inclusion of individuals with research software skills in projects that involve software development is highly beneficial, e.g. by improving the quality and sustainability of the research software developed. |
| Sectors | Aerospace, Defence and Marine,Chemicals,Digital/Communication/Information Technologies (including Software),Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | https://bristol.ac.uk/acrc/research-software-engineering/ |
| Description | This award aimed to help me work as part of a community to establish sustainable career pathways, funding, and training for Research Software Engineers (RSEs). This was achieved through talks, lobbying, participation in EPSRC Strategic Advisory Groups, demonstration of success at Bristol and working as part of a larger community. The result is that now, Research Software Engineering and Research Software Engineers are established as important members of research teams, and RSE groups now thrive at the majority of UK research-intensive Universities. Concrete examples of impact include the establishment of a sustainable and growing RSE group at Bristol, and my contribution to establishing the Society of Research Software Engineering (of which a member of my group is currently president). The Society has hundreds of paying members, and over 4000 active contributors to its Slack channel. This has now evolved with a growing number of international RSE groups now establishing (as listed here https://society-rse.org/international-rse-organisations). The establishment of RSE has directly impacted UK academics and industrialists whose research depends on UK scientific code. This was most evident during the pandemic, with RSE contributing to many of the key codes used for modelling. In my case, I worked closely with the group of Leon Danon, and completely overhauled and updated the MetaWards code (https://metawards.org). My work to improve software for cloud applications enabled researchers to rapidly leverage cloud resources for modelling the spike protein (e.g. see https://www.biorxiv.org/content/10.1101/2021.11.12.468428v1). Outside of COVID, I and my group improved the quality of biomolecular simulation code (e.g. BioSimSpace - https::/biosimspace.org and Sire - https://siremol.org), such that these are now robust and trustable enough to be used by the pharmaceutical industry for small molecule drug design. Software developed in this award has been commercialised by Cresset (a UK software company), and is now sold as part of the Flare package. Furthermore, subsequent to this award, we have formalised the links with industry by creating the OpenBioSim Community Interest Company (https://openbiosim.org). This is a community enterprise that provides development and maintenance support for open source software used by the pharmaceutical industry for biomolecular modelling. The flagship software for OpenBioSim are BioSimSpace and Sire. Companies now buy into OpenBioSim, which funds RSEs who develop and sustain the software. This has achieved the aim of maximising the return from EPSRC investment in software, as the initial EPSRC grant that funded BioSimSpace has resulted in a sustainably self-funding code that is now growing and having major impact (e.g. both as an industrial code and as a foundation for future software development applications from the HECBioSim and CCPBioSim academic communities). Finally, the biggest impact from this work has been the establishment and delivery of a complete and coherent training programme in programming, software engineering, data analysis and machine learning (https://bristol.ac.uk/acrc/research-software-engineering/training/ and https://milliams.com/courses/). These courses have a consistent style, being 3 hours in length, and following a described learning pathway with clear dependencies. The workshop material is fully online, often complemented with complete youtube videos, and is suitable for self-study, taught in-person classroom, or remote teaching. We have successfully delivered this material to thousands of individuals across the World. This was either via workshops for Bristol researchers (our programme has ~1000-2000 attendances per year) or via openly accessible workshops run via events, e.g. such as the JGI Data Week. These raised the profile of software engineering and software engineering best practice. I am sure that these will have contributed to many more researchers becoming empowered to code, gaining a love of programming, and learning how to write software in a sustainable and robust manner. |
| First Year Of Impact | 2017 |
| Sector | Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | Membership of EPSRC e-infrastructure SAT, 2017-2021 |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/sat/ |
| Description | Membership of the UKRI eInfrastructure Expert Group |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Amazon Cloud Computing Credits |
| Amount | $5,000 (USD) |
| Organisation | Amazon.com |
| Sector | Private |
| Country | United States |
| Start | 09/2019 |
| End | 03/2020 |
| Description | BBSRC 16ALERT Mid-range equipment initiative |
| Amount | £300,000 (GBP) |
| Funding ID | BB/R000484/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 07/2018 |
| Description | Computational Science and Engineering: Software Flagship Project Call |
| Amount | £645,752 (GBP) |
| Funding ID | EP/P022138/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 12/2019 |
| Description | EPSRC Impact Acceleration Award |
| Amount | £35,999 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2016 |
| End | 02/2017 |
| Description | EPSRC USA-UK RSE Travel Fund |
| Amount | £8,000 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 03/2018 |
| Description | Google Cloud Computing Credits |
| Amount | £4,000 (GBP) |
| Organisation | |
| Sector | Private |
| Country | United States |
| Start | 07/2019 |
| End | 10/2019 |
| Description | HUGS: a Hub for Uk Greenhouse gas data Science |
| Amount | £214,452 (GBP) |
| Funding ID | NE/S016155/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2019 |
| End | 02/2020 |
| Description | Microsoft Azure Sponsorship |
| Amount | $20,000 (USD) |
| Organisation | Microsoft Research |
| Sector | Private |
| Country | Global |
| Start | 07/2017 |
| End | 12/2018 |
| Description | Microsoft RSE Cloud Fellowship (awarded to team member, Matt Williams) |
| Amount | £4,000 (GBP) |
| Organisation | Microsoft Research |
| Sector | Private |
| Country | Global |
| Start | 11/2017 |
| End | 11/2018 |
| Description | OpenGHG: A community platform for greenhouse gas data science |
| Amount | £548,115 (GBP) |
| Funding ID | NE/V002996/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2020 |
| End | 08/2022 |
| Description | Oracle Cloud for Research Cloud Computing Credits |
| Amount | $26,000 (USD) |
| Organisation | Oracle Corporation |
| Sector | Private |
| Country | United States |
| Start | 04/2018 |
| End | 03/2020 |
| Description | SSI Fellowship (awarded to team member, Matt Williams) |
| Amount | £3,000 (GBP) |
| Organisation | University of Edinburgh |
| Department | UK Software Sustainability Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 12/2018 |
| Title | BioSimSpace 2019.1.0, 2019.2.0, 2019.3.0 |
| Description | BioSimSpace is an interoperable Python framework for bimolecular simulation. It helps researchers easily build interoperable workflow components for running complex biomolecular simulations. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | BioSimSpace has been used as the basis for many CCPBioSim training workshops, it has been downloaded 700 times and been published as a JOSS paper, and used to produce results for a soon-to-be-published paper produced in partnership with industry (http://dx.doi.org/10.26434/chemrxiv.11812053, "Automated Assessment of Binding Affinity via Alchemical Free Energy Calculations"). BioSimSpace is now part of the Cresset Flare package and underpins a new collaboration with UCB. |
| URL | https://biosimspace.org |
| Title | Brunel's Network |
| Description | A web application detailing the interactions and relationships between individuals who financed and engineered Brunel's three great steamships (SS Great Western, SS Great Britain and SS Great Eastern) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Web application was developed as part of a short collaboration with James Boyd of the Brunel Institute. This is being developed now into an interactive public exhibit at the SS Great Britain. It also led to a spin-off display showing the individuals and relationships involved in building Temple Meads train station and the Engine Shed. This is on permanent display at the Engine Shed, as part of the Brunel Trail. |
| URL | https://brunels-network.github.io/network/ |
| Title | Cluster in the Cloud |
| Description | Cluster-in-the-cloud provides on-demand, autoscaling, heterogeneous high performance computing clusters on a range of public cloud providers (Oracle, Google, Amazon). |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Cluster-in-the-cloud has been used by many research projects to provision and run the HPC cloud resources. This includes my contribution to outputs https://doi.org/10.1126/sciadv.aaw2853 and https://doi.org/10.1021/jacs.9b09055, as well as projects undertaken at other universities in the UK and abroad. The software was initially developed as part of a collaboration with Oracle, and has since been ported to Google and Amazon with financial support from those companies. The software is providing the foundation for the growth of new ways of using cloud to perform research. |
| URL | https://cluster-in-the-cloud.readthedocs.io |
| Title | MetaWards |
| Description | MetaWards implements a stochastic metapopulation model of disease transmission. It can scale from modelling local transmission up to full national- or international-scale metapopulation models. Please take a look at the features to see what MetaWards can do. Follow the quick start guide to see how to quickly get up and running using MetaWards to model your own custom disease or metapopulation model. Full Changelog: https://github.com/metawards/MetaWards/compare/1.6.0...1.6.1 |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Impact | Software is in use to model the spread of COVID, and to model uncertainty, e.g. as described here: https://uq4covid.github.io |
| URL | https://zenodo.org/record/5562737 |
| Title | MetaWards |
| Description | MetaWards implements a stochastic metapopulation model of disease transmission. It can scale from modelling local transmission up to full national- or international-scale metapopulation models. This is a Python port of the MetaWards package originally written by Leon Danon which was originally developed to support modelling of disease transmission in Great Britain and used to produce data that was used by SAGE to influence the Covid response. The Python port addressed the reproducibility, sustainability, robustness and extensibility of the original code, and has created a platform that now supports a community of epidemiologists who are using it to study the Covid spread. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | MetaWards is being used to model the spread of Covid, with the results used by epidemiologists as part of data that is fed through the SAGE. |
| URL | https://metawards.org |
| Title | Sire - 2016.1, 2016.2, 2016.3, 2016.3.1 |
| Description | Sire Molecular Simulation Framework 2016.X releases (2016.1, 2016.2, 2016.3, 2016.3.1) |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | The 2016 releases of Sire included enhanced parallelisation and optimisation to allow scaling on new multicore and massively multicore hardware, together with full production implementations of LigandSwap and Quantomm. Version 2016.X includes metrics collection code that shows that the 2016.X releases have been used over 70,000 times across 7 countries (including over 60 times in the US, ~250 times in Canada, and ~1500 times in Spain). Sire 2016.3.1 is being commercialised via a new collaboration with Cresset, with the waterswap tool being built into the new product "flare" (which is currently in beta release, and will be marketed at the 2017 Spring ACS Meeting in San Francisco. The software provides the foundation of the successful CCP-Biosim Software Flagship application to the EPSRC, and will form the basis of BioSimSpace, which will provide an underlying platform to support national and international collaborative biomolecular simulation software development and application. provided a much cleaner user interface, which encouraged uptake. It provided the proof-of-concept implementation of the LigandSwap method, which was refined and given a simple user interface such that it is now in use (papers describing this method are in production). Researchers at the University of Edinburgh have combined this software with the OpenMM dynamics software from the Pande group (Stanford) to give a GPU-accelerated MD capability. The software has been picked up by a pharmaceutical software company (Cresset), who are now working with me to create commercial software based on top of Sire. The software forms the basis of several derived software development projects (e.g. FESetup, Nautilus, Waterswap, Ligandswap) and also provides the foundation layer for the software projects described in my EPSRC RSE Fellowship. This software is the foundation for continued development (Sire 2016.X), and is now being used as the foundation of software to model the growth of bacterial cell colonies. Papers that I have produced based not the 2014.X versions of Sire include; Loeffler, H, Michel, J & Woods, CJ, 2015, "FESetup: Automating Setup for Alchemical Free Energy Simulations". Journal of Chemical Information and Modeling Woods, CJ, Shaw, KE & Mulholland, AJ, 2015, "Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein-Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase". Journal of Physical Chemistry B, vol. 119, pp. 997-1001 Woods, CJ, Malaisree, M, Michel, J, Long, B, McIntosh-Smith, S & Mulholland, AJ 2014, "Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water". Faraday Discussions, vol 169., pp. 477-499 |
| URL | https://siremol.org |
| Title | Sire 2017.1, 2017.2, 2017.3 |
| Description | Sire Molecular Simulation Framework 2017.X releases (2017.1, 2017.2, 2017.3) |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | The 2017 releases of Sire included improved file format support and molecular parsing code which has provided the foundation for the development of the BioSimSpace project. The new software includes optimisations for Intel Xeon Phi and newer Intel processors, including code needed to increase portability and support commercialisation of the "waterswap" and "proteinswap" applications that have been included in Cresset's Flare tool (https://www.cresset-group.com/flare/). Sire is now used commercially as part of Flare by companies around the World (including Australia and China). Analytics at https://siremol.org/analytics show that the 2017.X versions of Sire have been used over 60,000 times over the last year, including over 10,000 times in the USA and over 8000 times in China. |
| URL | https://siremol.org |
| Title | Sire 2018.1.0, 2018.1.1, 2018.2.0 (2018) |
| Description | The 2018 releases of Sire included improved file format support and molecular parsing code which has provided the foundation for the development of the BioSimSpace project. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Analytics at https://siremol.org/analytics show that the 2018.X versions of Sire have been used over 36,000 times over the last year. |
| URL | https://siremol.org |
| Title | Sire 2019.1.0, 2019.2.0, 2019.2.1, 2019.3.0 |
| Description | Sire molecular simulation framework, used as the basis for many tools, e.g. SOMD, FESetup and BioSimSpace. The 2019.X versions of Sire have been used over 180,000 times (https://siremol.org/analytics/versionchart.html). |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | This year's versions resulted in new packages that were auto-built for conda. This made it easier to package and distribute Sire, as well as for building new software on top of Sire. In particular, BioSimSpace was able to use Sire successfully as a dependency. |
| URL | https://siremol.org |
| Description | Chair of the Second Research Software Engineering Conference (2017) |
| 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 | Over 220 international research software engineers, members of industry and representative from UK research councils attended this two-day workshop which I chaired in September 2017. The conference featured a mix of talks and practical workshops, and brought together research software engineers from around the world to share best practice, discuss policy on driving research software engineering careers, and learn new techniques. The conference was sponsored by Microsoft, Canarie, nVidia, EPSRC, Lenovo amongst others, and was well received (see https://rse.ac.uk/conf2017). The third conference will be held in September 2018. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://rse.ac.uk/conf2017 |
| Description | Co-organiser of the International RSE Leaders Meeting |
| 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 | Research Software Engineer group leaders from around the World attended a two-day meeting to discuss and share best practice on how to develop, support and grow RSE careers and improve the quality of international research software. The meeting included talks and discussion sessions. The results included the growth and initiation of RSE communities in Germany, Sweden and The Netherlands, and increasing internationalisation of the UK RSE communication channels (e.g. increasing international engagement with the UKRSE Slack channel and mailing list). |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://rse.ac.uk/rse-international-leaders-meeting |
| Description | EPSRC Blog post |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I was invited to write a blog post which was published on the EPSRC website. The post described my recent visit to the supercomputing centre in China, and discussed the power of software to drive innovation. I don't know how many people read this post, nor how it was received. However, I believe this kind of engagement is important as it helps communicate the role of research software engineers and the importance of research software to a wider audience. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.epsrc.ac.uk/blog/the-power-of-software-to-drive-innovation/ |
| Description | First Conference of Research Software Engineers |
| 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 | I was on the organising committee (workshop chair and website manager) for the first conference of research software engineers (RSEs). The purpose was to bring together RSEs, funders, sponsors and other stakeholders to discuss issues around research software, participate in talks and hands-on training workshops. 202 people from 14 different countries attended over two days at the Manchester Museum of Science and Industry. Response from the feedback survey showed that 95% of responders would come again to the conference, and it scored 4.3 out of 5. The majority of the attendees came from a background in Physical Sciences (30%), Computer Sciences (18%) and Biological Sciences (17%). The conference sparked discussions and shared knowledge. As a direct result, a UKRSE Slack channel was set up which has over 250 active members, and a second conference (which I will chair) is being arranged for September 2017. Feedback from the conference can be viewed and . |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://ukrse.github.io/conf2016.html |
| Description | Introduction to Python for Data Scientists Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | A follow-up to the earlier version control workshop, this was a workshop teaching Python as an introduction to Data Science. About 40 researchers and local industry representatives attended, gaining knowledge in how to use Python for analysing data. This has further grown the nascent RSE South West network |
| Year(s) Of Engagement Activity | 2019 |
| Description | Python training workshop in Bath |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | A two-day Python training workshop in Bath attended by about 50 postgraduate students from across the GW4 area. This upskilled the researchers in Python and software engineering best practice, as well as helping form the nascent RSE South West network |
| Year(s) Of Engagement Activity | 2019 |
| Description | Talks Chair of the 2019 Research Software Engineering Conference |
| 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 Fourth RSE conference brought together 420 international delegates over a three day meeting to discuss all aspects of research software engineering. This helped grow the RSE community, with RSE Worldwide within the conference showcasing the establishment of RSE groups and societies across many countries. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://rse.ac.uk/conf2019 |
| Description | Training Workshop (Bristol) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Organised and taught a two-day programming and data analysis training workshop at Bristol attended by 40 PhD and PDRA researchers from the South West (GW4). The workshops taught software engineering best practice, including version control, testing, good software design, data analysis and documentation. The attendees reported that they learned a lot and that they would adopt the best practice that they learned in their own research. The workshop material has been developed so that we can now run this workshop twice yearly, thereby reaching a large number of researchers. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://chryswoods.com/python_and_data |
| Description | Training Workshop (Manchester) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | 15 Phd and PDRA researchers attended a one-day parallel programming workshop that I ran at Manchester. The workshop taught parallel programming in C++. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Training Workshop (Sheffield) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | 15 students attended a two-day programming workshop I ran in Sheffield. This provided advanced knowledge on parallel programming techniques in C++ (including vectorisation and multicore programming) to PhD and PDRA researchers in the Sheffield and surrounding area. The students reported increased knowledge of these programming techniques and a desire to use them in their own research software. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Training workshop in Version Control at the University of Exeter |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Training workshop in Version Control run at the University of Exeter, which both resulted in upskilling researchers and local industries in software engineering good practice as well as incubating a regional RSE South West network. This led to requests for a data science workshop which we ran later in the year (June - this workshop was in March) |
| Year(s) Of Engagement Activity | 2019 |
| Description | nVidia Deep Learning Ambassador Training Workshop |
| 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 | I worked with nVidia to organise and run a Deep Learning Ambassador Training workshop. The aim was to "teach the teachers", by providing training material to research software engineers from around the UK so that they could, in turn, teach deep learning / AI to researchers at their own institutions. We have over 30 research software engineers attend, all of whom pledged to run workshops for researchers at their own institutions. We will be using the material ourselves to run Deep Learning workshops at Bristol in June, and are planning on using the material to run a national deep learning workshop in the summer. |
| Year(s) Of Engagement Activity | 2018 |