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.

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.
 
Description The software developed during this award has been commercialised by Cresset (a UK software company), and is now sold as part of the Flare package. The software is used by pharmaceutical and agrochemical companies to help design small molecule inhibitors.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description Membership of EPSRC e-infrastructure SAT
Geographic Reach National 
Policy Influence Type Participation in a 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 advisory committee
 
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 Academic/University
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 Academic/University
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 Academic/University
Country United Kingdom
Start 09/2017 
End 03/2018
 
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 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 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
 
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 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 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