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Welcome to the Fourth Conference of Research Software Engineering, held at the University of Birmingham. For directions to and during the event, see the campus maps page.

In the Aston Webb Building near to the registration/reception desk, a cloakroom is available in room G30 along with a quiet room in G31.

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Monday, September 16
 

12:30

HPC Champions Workshop - Colocated with RSEConUK2019
Following the successful HPC Champions/Tier-2 HPC Workshop @ RSECon18 we will again be co-locating with the main conference for an afternoon of talks and discussion.  This half day workshop is organised by James Grant (Bath) and Andy Turner (Edinburgh) funded by the Society of Research Software Engineering.

Registration is separate to the RSEConUK registration and can be found HERE. If you would like to contribute to the workshop or there is a topic you would like to suggest for discussion please indicate in your registration.

Event Address: University of Birmingham, venue to be determined.

Contact us: hpc.champions@gmail.com

HPC Champions has evolved from Archer Champions (https://www.archer.ac.uk/community/champions/) which was originally funded through an Outreach Grant.


Speakers
avatar for James Grant

James Grant

Research Software Engineer, University of Bath


Monday September 16, 2019 12:30 - 17:30
TBA

19:00

Pre-Conference summer buffet and drink reception hosted by Google
Join us for the pre-conference get together at the High Field pub in Edgbaston hosted by Google.

For delegates who confirmed their attendance tonight in the online registration form, a named voucher will be available for you near the pub entrance giving you the choice of a beer, glass of wine or prosecco or a soft drink. For those who have decided to come along on the spur of the moment, make yourself known to Claire to get a voucher.

From 7:30pm to 9pm, a summer buffet will be served. Don't all queue at once!

Menu
Laverstoke Mozzarella, Heritage Tomato & Basil Salad
Crispy Chilli Beef
Smoked Salmon Rillettes & Crisp Bread
Free-range Mojo Chicken
Halloumi Fries
Dorset Charcuterie & Cornichons
Spinach Pakoras & Coconut Yoghurt
Spiced Tomato Houmous & Pitta Buffalo
Cauliflower & Chipotle
Courgette & Feta Salad
Buttermilk Chicken & Chipotle
Ham Hock & Piccalilli
Beetroot, Feta & Rocket Wrap, Cucumber & Mint
Rustic Chips
Green Salad & Soft Herbs, Avocado Dressing
Buttered New Potatoes


Monday September 16, 2019 19:00 - 23:00
The High Field Pub 23 Highfield Road, Edgbaston, B15 3DP
 
Tuesday, September 17
 

08:00

Registration (Foyer)
Please register and pick up your badge etc. from the registration desk. Tea, Coffee and water will also be available in the Great Hall from 8am to 9am.

In the Aston Webb Building near to the registration/reception desk, a cloakroom is available in room G30 along with a quiet room in G31.

Tuesday September 17, 2019 08:00 - 09:00
6. The Great Hall Aston Webb Building

09:00

Welcome and Introduction
Moderators
avatar for Andrew Edmondson

Andrew Edmondson

Research Software Group Leader, University of Birmingham
I'm a research software engineer, theologian and mathematician. I am the Programme Chair of RSEConUK 2019 and chair of the Power AI User Group.
avatar for Claire Wyatt

Claire Wyatt

Community Manager for Research Software Engineering, Software Sustainability Institute / University of Southampton
Talk to me about events, training or networking that you'd like to see happen in the RSE Community.

Tuesday September 17, 2019 09:00 - 09:30
1. Bramall - Elgar Concert Hall Aston Webb Building

09:00

Posters available to view from 9am to 3pm
Tuesday September 17, 2019 09:00 - 15:00
10. Mezzanine Floor, (First floor), Bramall Foyer Bramall Elgar Concert Hall, Above Costa coffee

09:30

Keynote
Speakers
avatar for Andy Stanford-Clark

Andy Stanford-Clark

Chief Technology Officer for IBM in UK and Ireland, IBM
Prof Andy Stanford-Clark is the Chief Technology Officer for IBM in UK and Ireland. He is an IBM Distinguished Engineer and Master Inventor with more than 40 patents.Andy is based at IBM's Hursley Park laboratories in the UK, and has been working in the area that we now call the Internet... Read More →


Tuesday September 17, 2019 09:30 - 10:30
1. Bramall - Elgar Concert Hall Aston Webb Building

10:30

Refreshments
Tea, Coffee, water and biscuits will be available in the Great Hall.

Tuesday September 17, 2019 10:30 - 10:55
6. The Great Hall Aston Webb Building

11:00

#1A1 - Engagement and Outreach - Public engagement and RSEs - A vital role?
Research institutions are becoming increasingly aware of the need to share the benefits of their research with the public; a clear plan for disseminating information to and learning from the public (public engagement) is now a required element for all major UK research funding agencies.

RSEs are often viewed as external to the public engagement process, but their skills hold great potential to help researchers facilitate knowledge exchange with the public. For example, research results are often disseminated through RSE-developed dashboards and databases, citizen science projects often rely on technical platforms developed by RSEs and data visualisation skills can transform the way public understand complex topics.

In this talk, I will showcase a range of projects where RSE input has led to excellent public engagement (and discuss the strengths and limitations of each) with the aim of inspiring RSEs to consider their work in a public engagement context in the future. This will help empower the RSE to become more aware of the vital role they play in this process, and ultimately lead to the development of technical tools that are better designed from a public engagement viewpoint.

Speakers
avatar for Kirsty Pringle

Kirsty Pringle

Model Domain Exper, Center for Environmental Modelling and Computation, University of Leeds
I am an atmospheric scientist and RSE, specialising in helping people use weather and climate models for research into climate change and atmospheric pollution. I work with a domain-specific technical support group called the Centre for Environmental Modelling And Computation (https://www.cemac.leeds.ac.uk... Read More →


Tuesday September 17, 2019 11:00 - 11:25
1. Bramall - Elgar Concert Hall Aston Webb Building

11:00

#1D1 - Legacy Software - A case study in optimisation of legacy software
An old serial program for Lattice Field Theory Simulations, initially written in fixed-form Fortran during decades of research work, needed to be optimised for modern architectures. In this talk I will describe the challenges, the decisions, and the steps we took in order to improve its performance and its scientific output (which is a multi-level optimisation problem), discuss the tools used and the experience we had with them (Intel VTune, ITAC, the Scalasca suite and the BSC Performance Tools), and report our - sometimes surprising - findings.

Speakers

Tuesday September 17, 2019 11:00 - 11:25
4. Aston Webb, Room WG12 Aston Webb Building

11:00

#1B1 - Reproducible Research - Reproducible Research Compendia with rrtools
Strides towards reproducibility have highlighted the importance of integrating computations and code used in research with the documents that describe and rely on them. However, we still lack formal frameworks, conventions and simple tools for everyday researchers to achieve this.

In 2004, Gentleman & Temple Lang introduced the concept of a research compendium as both a container for the different elements that make up a research paper and its computations (i.e. text, code, data, ...), and as a means for distributing, managing and updating the materials.

For R users, package rrtools (https://github.com/benmarwick/rrtools) provides instructions, templates, and functions for making a basic compendium suitable for writing reproducible research with R. The resulting compendia are based on R package structure, enabling access to powerful developer tools for recording project metadata, developing, checking and testing code, and distributing materials. In this walkthrough I’ll demonstrate producing a research compendium around a reproducible manuscript, by combining code, text and data using rrtools and friends.

Speakers
avatar for Anna Krystalli

Anna Krystalli

Research Software Engineer, University of Sheffield


Tuesday September 17, 2019 11:00 - 11:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building

11:00

#1C1 - Mentoring and Inclusivity - Concrete ways to build an inclusive workplace
Do you genuinely care about building an inclusive workplace, but feel unable to change the system? Do you care about diversity, but there isn’t a lot you can do on your own about representation or hiring within your organization? Do you want to be an ally, but don’t know how to be effective? Are you unsure how your intervention would be perceived? Having successfully improved diversity in your workplace, how would you give everyone a sense of belonging? Come along to this discussion, where we will discuss a few concrete actions that you can take, alone or with others, to build a more inclusive environment. We will illustrate the actions supported by anecdotal evidence and research.

This will be a discussion led by a panel consisting of representatives from academia and industry, covering a wide range of backgrounds and experiences. You can expect to take away actionable ideas to help you build an inclusive workplace.

Speakers
avatar for Pashmina Cameron

Pashmina Cameron

Sr RSE Lead, Microsoft Research Cambridge
Machine learning, Computer vision, NLP, Healthcare, C++, Python
avatar for Camilla Longden

Camilla Longden

Research Software Engineer, Microsoft Research
I'm an RSE at Microsoft Research in Cambridge. I work in the Deep Learning Engineering team in the ADA (All Data AI) group. I am also interested in diversity and inclusion in the technology sector.


Tuesday September 17, 2019 11:00 - 11:40
5. Nuffield Building, Room G17 Nuffield Building

11:30

#1A2 - Engagement and Outreach - BEAR Software – Coaching - Teaching Researchers to Fish
There is the saying: ‘Give a man a fish and feed him for a day; teach a man to fish and feed him for a lifetime’. This saying applies to researchers who are writing research software. Even with a RSEs at a university, researchers will continue to write a lot of research software and it is important for RSEs to positively impact this software. By working with researchers, we can upskill researchers so that they write high quality software – leading to the SSI’s ‘Better Software, Better Research’.

I will talk about the coaching programme we provide to researchers, where we engage with researchers in several ways to improve the research software being written and to make it easier for this software to be distributed and reused. We offer a variety of training, coaching, and mentorship to all levels of researchers – from those to just starting their research career to senior researchers. I will present case studies detailing some of the coaching we have provided and how this has improved the research software being written at this university.

Speakers
SB

Simon Branford

Research Software Engineer, University of Birmingham


Tuesday September 17, 2019 11:30 - 11:55
1. Bramall - Elgar Concert Hall Aston Webb Building

11:30

#1D2 - Legacy Software - Refactor, Rewrite or Retire
How do we define legacy software?
Code that falls into this category can be typically classified by a lack of tests, or use of outdated practices, including unsupported dependencies, or having a code base written in an obsolete programming language. Whilst this list is not exhaustive, these are usually the signs that software is going to cause you issues when it comes to attempting to extend or scale the code.

Characterisation of code then falls into two simple categories, legacy code, and not legacy code. With no clear definition on legacy software, the boundary between the two is far from clear, and is constantly moving. However, one thing that remains clear and consistent is that every piece of software will encounter the issue of migrating legacy systems in its life cycle.

Generally, there are three possible solutions when dealing with legacy software: refactor, rewrite, or retire. All three options should always be considered when reaching that point in the software development life cycle, and this talk examines the costs and benefits for each. A strong focus on testing is leveraged in this talk when considering either rewriting and refactoring and establishing a good set of tests is paramount when using these approaches.

Speakers
avatar for Thomas Stainer

Thomas Stainer

UKAEA
Coming from a particle physics background, I learnt to program during my PhD, where I quickly realised how powerful programming is as a skill. Since then, I have oscillated between the private and public sector, working in petrochemical and IT security industries. Currently I work... Read More →


Tuesday September 17, 2019 11:30 - 11:55
4. Aston Webb, Room WG12 Aston Webb Building

11:30

#1B2 - Reproducible Research - Towards a production-ready solution for reproducible articles
With Substance and Stencila, eLife has been developing the Reproducible Document Stack (RDS), an open technology stack that will enable researchers to publish reproducible manuscripts. Its motivation came from recognising one of the key problems with the current established format of research articles: research methods are not generally described in sufficient detail to allow other researchers to faithfully repeat key experiments. This is in part due to the increasing complexity of modern research, in particular in its computational methods.

In this walkthrough, I will demonstrate how a researcher can create a reproducible article with Stencila Desktop, an open-source, easy-to-use manuscript editor with combines the traditional authoring workflows with R and Python code blocks that can analyse table data and generate live interactive plots. The reproducible article can be viewed, edited and executed from within a web browser; plots can be updated live by re-running the embedded code. I will discuss the underlying technologies of the article, and our future plans to develop RDS into a scalable, production-ready solution. We invite feedback from the community on the project’s potential functionalities and development roadmap.

Speakers
avatar for Maël Plaine

Maël Plaine

Product Manager, eLife
Maël Plaine developed his interest in building digital products while working in the music industry. He joined eLife as Product Manager for the organisation’s journal platform and Libero Publisher. He is now also responsible for the development of Libero Data Hub: a platform for... Read More →


Tuesday September 17, 2019 11:30 - 11:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

11:45

#1C2 - Mentoring and Inclusivity - RSE mentoring scheme: a discussion
Mentoring supports professional and personal development, helping people to identify and pursue goals, respond to challenging situations, and get broader perspectives. This may be through 1:1 interaction or in small groups of peers, and may use traditional informative mentoring, coaching, or peer-support techniques. An RSE mentoring scheme would help RSEs who do not have access to mentoring within their institution, want external contacts or who are looking for advice related to RSE activities. It could be particularly valuable at times of transition such as transferring from academic track to an RSE role or moving into leadership. This panel will engage the community in the creation of a scheme by raising awareness, promoting discussion and gathering input and feedback. Open questions to answer include whether mentoring should be in groups or 1:1, which communities mentors should be drawn from and how they could be trained, how best to serve under-represented groups, how participants should be matched and what infrastructure support is needed. The panel will include people with experience as mentors, as mentees and in setting up and running schemes to give various perspectives on mentoring and how to implement it.


Panelists (in alphabetical order):
  • Toni Collis, WHPC, UK
Dr Toni Collis is the Director and CEO of Collis-Holmes Innovations and Chair of Women in High Performance Computing (WHPC). Toni is a strategic manager, and a Leadership & Success Coach. As an HPC professional the focus of her work has been on enabling those without detailed training in computer science and HPC to still use supercomputers and developing a pipeline of inclusive technology leaders. Toni has worked on a variety of mentoring programmes including redesigning the mentoring programme for the International HPC Summer School and helping to put in place a new mentoring programme for WHPC over the last 12 months that supports women internationally in their earliest career stages to mentoring for women in senior management. Toni specialises in strategy for HPC & workforce inclusion in Tech and providing Leadership Coaching for women in STEM.
  • Catherine Jones, STFC, UK
Catherine Jones leads the Software Engineering Group in the Scientific Computing Department at STFC.  She has a computing degree, is a member of the British Computer Society and a chartered Librarian. Her Group provides Anvil, for research software testing ; experimental research data management systems and STFC publication and data repositories.   Her personal research interests are the digital curation of software & data; linking research outputs (data, publications and software) and career paths for Research Software Engineers. She is a member of the SSI Advisory Board, the Research Software Alliance​ organising committee and the organising committee for the SuperComputing19 Early Careers Programme.  She has managed staff for over twenty-five years and both been mentored and has mentored other staff during her career at STFC. She has also recently been professionally coached on enhancing her female leadership style in a male environment.
  • James Hetherigton, Turing Institute, UK
James is the Director of Research Engineering at the Alan Turing Institute, the UK’s national institute for data science and artificial intelligence. James directs the "Tools, Practices and Systems" research programme within UK Research and Innovation's strategic priority programme "AI for Science, Engineering, Health and Government".
James leads a team of research software engineers and data scientists contributing to a huge range of data- and compute-intensive research. They build and use tools to analyse and present large datasets, and create complex models running on state of the art supercomputers.
He was the founding head of UCL’s Research Software Engineering Group, the first such group in the UK. Fields addressed included ancient Mesopotamian history, graph theoretical approaches to modeling chemical catalysis, intensive care big data, compressive sensing for the Square Kilometer Array, the history of trans-oceanic journalistic exchanges, data centric engineering, brain blood flow simulations and DNA crime scene analysis statistics.
  • Mateusz Kuzak, DTL, Netherlands
Mateusz Kuzak is a Scientific Community Manager at the Dutch Techcentre for Life Sciences (DTL), where he works at the interface of training, technology and data platforms and the research community in the Netherlands. Before joining DTL, Mateusz was building research software at the Netherlands eScience Center in collaborative projects with domain scientists. At the Center Mateusz also helped to develop the training program around essential computing skills offered to project partners. Before becoming Research Software Engineer, he worked in the field of Biophysics spending lots of time with microscopes. Mateusz have been also involved in the Carpentries community as an instructor, trainer, mentor and Steering Committee member.
  • Aiman Shaikh, STFC, UK
Aiman Shaikh is driven towards making innovative discoveries in the field of technology. Currently working as a Research Software Engineer at the Science and Technology Facilities Council (STFC) Hartree Centre, Aiman is motivated by applying her expertise to enterprise by facilitating technological advancements and unlocking value for industry through high performance computing. Enjoying both research and practical elements of her role, Aiman is driven to make a positive impact within the field by applying technology to solve industry challenges and advocating for female participation in both underdeveloped and developing countries. By presenting her work and being an active member of the HPC community, Aiman feels that her presence can encourage other female developers and software researchers to take up careers within the field.

Speakers
avatar for Alejandra Gonzalez-Beltran

Alejandra Gonzalez-Beltran

Data Management Team Lead, Science and Technology Facilities Council
avatar for Mozhgan Kabiri Chimeh

Mozhgan Kabiri Chimeh

Research Associate/RSE, University of Sheffield
avatar for Anna (Ania) Brown

Anna (Ania) Brown

RSE, University of Oxford
avatar for Alys Brett

Alys Brett

Head of Software Engineering Group, UKAEA
Current chair of the Society of Research Software Engineering.I lead the software engineering group at the UK's national lab for nuclear fusion where we have teams working on experimental data systems and tools, database and web applications and a fast-growing new RSE projects team... Read More →
avatar for Jonathan Cooper

Jonathan Cooper

Head of Research Software Engineering, UCL
PR

Paul Richmond

Director of RSE, University of Sheffield


Tuesday September 17, 2019 11:45 - 12:25
5. Nuffield Building, Room G17 Nuffield Building

12:00

#1A3 - Engagement and Outreach - Developing and using a cluster of Raspberry Pis for outreach
The Supercomputing Wales project has as one of its goals increasing the public understanding of High-Performance Computing in Wales. To further this ambition, the RSE team at the Swansea Academy of Advanced Computing agreed to run a stand at the Swansea Science Festival 2018. To this end, we assembled a cluster of 16 Raspberry Pi single-board computers, and developed software to demonstrate some of the principles of parallel computing as well one of as the types of problem that the supercomputer in Swansea is used for in research. In this talk, we will describe the process of designing and constructing both the hardware and the software, and some of the challenges we encountered along the way, as well as discussing how well it works as a scaffold to discussions around parallel computing with members of the general public.

Speakers
avatar for Ed Bennett

Ed Bennett

Research Software Engineer, Swansea Academy of Advanced Computing, Swansea University


Tuesday September 17, 2019 12:00 - 12:25
1. Bramall - Elgar Concert Hall Aston Webb Building

12:00

#1D3 - Legacy Software - Launching Java Applications into the Future
Over the years, the Java runtime platform has been hardened against a number of security vulnerabilities. Each time, maintainers have had to change their practices in order to ensure applications remain accessible to users.

In the first quarter of 2019, the Jalview (www.jalview.org) team migrated their mature interactive application from Java 1.8 to Java 11. It required some radical changes. Build, deployment, installation and launch mechanisms were recoded. Getdown (https://github.com/threerings/getdown) was adopted to replace Java Webstart, and adapted to give a hopefully seamless experience with an "install once, works forever" approach. JRE packaging methods were developed to allow over-the-air updates in preparation for future Java releases. We’re now adapting Getdown further to support "channels" so that the user can easily switch between a stable release, development release, or access older versions of Jalview to aid reproducibility.

I’ll examine the issues we encountered when migrating an interactive graphical desktop Java application relied on by thousands of researchers and educators to Java 11. I’ll also evaluate whether our new deployment model meets the future needs of our broad community of users.

Speakers
avatar for Ben Soares

Ben Soares

Research Software Engineer, University of Dundee School of Life Sciences


Tuesday September 17, 2019 12:00 - 12:25
4. Aston Webb, Room WG12 Aston Webb Building

12:00

#1B3 - Reproducible Research - Interoperable software for reproducible research
In most research communities there is not a single, unified software-framework. Instead, researchers are presented with a collection of competing packages from which they pick and choose the functionality that they desire. Interoperability between packages is often poor, with incompatibilities between file formats, hardware, etc. This leads to brittle workflows, poor reproducibility, and lock in to specific software. For the biomolecular simulation community, our solution has been the introduction of an interoperable framework that collects together the core functionality of many packages and exposes it through a simple Python API. By not choosing to reinvent the wheel, we can take advantage of all the fantastic software that has already been written, and can easily plug into new software packages as they appear. Our software can convert between many common molecular file formats and automatically find packages available within the environment on which it is run. I will show how this allows the user to write portable workflow components that can be run with different input, on different environments, and in completely different ways, e.g. command-line, Jupyter notebook, Knime.

Speakers
avatar for Lester Hedges

Lester Hedges

Research Software Engineer, University of Bristol


Tuesday September 17, 2019 12:00 - 12:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building

12:30

Lunch sponsored by Digital Science
A cold fork buffet will be provided. Menu tbc soon.

Tuesday September 17, 2019 12:30 - 13:25
6. The Great Hall Aston Webb Building

13:30

#2A1 - Careers and Culture - (Research Software) Engineering is not Research (Software Engineering)
With over a decade of experience in industry as a software engineer, architect, and manager, I was expecting a move into research software engineering to involve a straightforward application of my experiences and skills to a new domain. In fact I quickly discovered that the contexts and motivations are different enough that even when we adopt the same practices, it's often for very different reasons. Research Software Engineering needs a different set of guiding values and principles from industrial software engineering; Agile software development and Software Craftsmanship do not supply those values.

Speakers
avatar for Graham Lee

Graham Lee

Head Labrarian, Labrary Ltd.
I make it easier and faster to make high-quality software that respects people's privacy and freedom. You can find me in universities or in companies, but that's probably what I'll be doing. Talk to me about continuous delivery, devops, team performance, measuring success, Python... Read More →


Tuesday September 17, 2019 13:30 - 13:55
1. Bramall - Elgar Concert Hall Aston Webb Building

13:30

#2D1 - Revitalising Legacy Languages - Teaching an old dog new tricks - object-oriented programming in Fortran
RSEs often need to work with code written in Fortran. Though most commonly thought of as a procedural language, modern Fortran features fully-fledged object-oriented programming (OOP) complete with inheritance, encapsulation, and polymorphism. This talk introduces the syntax and philosophy behind OOP in Fortran to those familiar with older versions of the language, showing how it naturally extends pre-existing features. It will also compare the Fortran approach to OOP to those used in other programming languages in a manner which can be understood by non-Fortran developers. Finally, this talk will reflect on the advantages and disadvantages of using OOP in Fortran and under what circumstances this is an appropriate paradigm.

Speakers
avatar for Chris MacMackin

Chris MacMackin

Research Software Engineer, UKAEA
I am part of the newly-formed RSE group at the UK Atomic Energy Authority. We assist researchers in developing new software and promote best practices within the organisation. My interests include numerical methods and different programming paradigms. I am very knowledgeable about... Read More →


Tuesday September 17, 2019 13:30 - 13:55
4. Aston Webb, Room WG12 Aston Webb Building

13:30

#2B1 - Useful Tools and Libraries - A beginner's guide to Kivy: a multi-touch GUI library for Python
Kivy is an open-source Python library for rapid development of applications that make use of innovative user interfaces, such as multi-touch apps, and runs on a wide range of platforms. In this walkthrough, I will introduce the Kivy framework from a user's perspective, and construct a very simple application. Along the way, I will highlight some of the positive and negative features in my view, and demonstrate a selection of the available functionality. I will also talk briefly about a project I have recently worked on using Kivy, and demonstrate the final results, in order to demonstrate the capabilities of the library more fully.

Speakers
avatar for Sam Cox

Sam Cox

Research Software Engineer, University of Nottingham


Tuesday September 17, 2019 13:30 - 13:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

13:30

#2C1 - Policy and Culture - Software development best practices - Why aren’t we implementing them?
Software developer guidelines have been around for a while now. Many groups and communities have created custom guidelines and teaching has increased throughout all disciplines, with dedicated projects leading the mission to encourage uptake. Nevertheless, adoption is slow.
In most cases, research projects produce prototypes or demonstrators. In the quest to create and innovate new tools and solutions, software quality is often overlooked. This causes a cemetery of research software produced through grants that never reached a state of technological stability and quality that enables reuse and reproducibility.
At the same time, awareness of existing best practices and quality criteria is rising throughout the community, with limited uptake for many practices. This discrepancy is being felt by the panellists in various positions.
The aim of the panel if to identify reasons for this and sketch possible scenarios to change this status quo. It is becoming more and more clear that only by recognising and crediting software as a dedicated research product as well as defining and enforcing requirements any change is possible. These aspects need to be implemented from the individual level up to enforcement by policy makers and funders.

Speakers
avatar for Anna Krystalli

Anna Krystalli

Research Software Engineer, University of Sheffield
avatar for Stephan Druskat

Stephan Druskat

RSE, SER, PhD candidate, German Aerospace Center (DLR)
I'm a Research Software Engineer, working in linguistics, and a PhD candidate in Software Engineering at the German Aerospace Center (DLR) and the Computer Science Department at Humboldt-Universität zu Berlin in Berlin, Germany. In my work, I focus on research software sustainability... Read More →
avatar for Carsten Thiel

Carsten Thiel

CESSDA ERIC
avatar for Lucy Whalley

Lucy Whalley

PhD candidate, Imperial College London
I'm a PhD candidate in computational materials science, and much of my time is spent writing post-processing scripts to analyse the output of supercomputer calculations (turning numbers --> physics). Before my PhD I taught mathmatics in a variety of contexts: prisons, primary schools... Read More →


Tuesday September 17, 2019 13:30 - 14:10
5. Nuffield Building, Room G17 Nuffield Building

14:00

#2A2 - Careers and Culture - From Trainee to Director - An Institutional RSE Career Pathway
RSE perform a complex mix of research and service provision that has to fit into career paths in academia. This University has developed and implemented a career pathway tailored to RSE as part of its Digital Research Strategy. A new team was formed in 2018 by merging and expanding existing RSE-like structures into a dedicated support facility outside academic structures of faculties and schools. Job profiles reflecting a professional services-style of working in a research context were created. These start at Trainee Level (Digital Research Graduate Programme), from where role holders can progress to become established RSE team members (Digital Research Scientist). A set of senior role profiles allows further progression with a focus on managerial (Digital Research Service Team Leader), academic and research-driven (Senior Research Data Scientist), or professional services (Senior Digital Research Scientist) responsibilities. A senior management role with strategic responsibilities (Head of Digital Research Service) leads the team and reports to the director of the Digital Research division. As far as we know, this University is the first to incorporate a career path that recognises distinct characteristics of RSE roles.

Speakers
avatar for Jurgen Mitsch

Jurgen Mitsch

Digital Research Service Team Leader, University of Nottingham
The University of Nottingham's Digital Research Service (DRS) is a dedicated, core facility to support researchers and improve research quality. 18 RSE provide bespoke, project-based support in Data Science/Data Analytics, Bioinformatics and Software Engineering.The DRS enable, improve... Read More →


Tuesday September 17, 2019 14:00 - 14:25
1. Bramall - Elgar Concert Hall Aston Webb Building

14:00

#2D2 - Revitalising Legacy Languages - Wasm! and the JavaScript is gone. What is WebAssembly and what can it offer research software?
WebAssembly (or Wasm) is a bleeding edge technology promising to massively expand the world of client-side web development outside the constraints of JavaScript, with potential for wider use as a universal sandboxed virtual machine runtime.

As a high-performance compilation target for the web, Wasm has potential applications in visualisation and performance-critical applications; I’ll explore these and other possible applications for research software. I’ll discuss the current state of Wasm, potential pitfalls and give an overview of the roadmap for the future.

Speakers
avatar for Drew Silcock

Drew Silcock

Research Software Engineer, STFC Hartree Centre


Tuesday September 17, 2019 14:00 - 14:25
4. Aston Webb, Room WG12 Aston Webb Building

14:00

#2B2 - Useful Tools and Libraries - Do you want to change the world (wide web)?
The web platform is constantly growing and evolving making it an exciting area to work in. However it is also frustrating as new features aren't always supported in all browsers. Even more frustrating is when implementations of features differ between browsers, making development and testing an arduous process. If only there was a way we could help...

But wait, there is!

In this session I will introduce attendees to the "web-platform-tests" project - a W3C-coordinated open source suite of regression tests to improve the web platform. We'll explore the project, and get hands-on by running some tests.

Attendees will get the most out of the session if they have some experience of web development, but anyone is welcome.

Speakers
avatar for Richard Williams

Richard Williams

Senior Software Engineer, University of Manchester


Tuesday September 17, 2019 14:00 - 14:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building

14:15

#2C2 - Policy and Culture - Creating Impact from research - an opportunity for RSE career development
The Research Excellence Framework (REF) in 2014 was the first national exercise to assess the impact of research outside of academia. UK higher education institutions (HEIs) submitted over 6,000 Impact Case Studies to demonstrate the benefit to society, the economy or the environment that occurred as a result of the research. The 2021 REF exercise further prioritises impact, and many HIEs are looking for opportunities to identify and maximise the impact of their research on society. This offers an exciting opportunity for RSEs, who are often critical to the translation of research into impact: RSEs that demonstrate their role in the creation of impact can gain additional career opportunities, improved recognition, evidence for promotion application and access to additional funding routes.

The panel will include expert RSEs and experienced academics who will share lessons learnt from the 2014 exercise and their plans for the 2021 exercise. Discussions will be centered around understanding of the importance of Impact on careers and funding for RSEs, advice on ways to effectively demonstrate Impact and lobby for inclusion of RSE work in the next REF exercise.

Speakers
avatar for Kirsty Pringle

Kirsty Pringle

Model Domain Exper, Center for Environmental Modelling and Computation, University of Leeds
I am an atmospheric scientist and RSE, specialising in helping people use weather and climate models for research into climate change and atmospheric pollution. I work with a domain-specific technical support group called the Centre for Environmental Modelling And Computation (https://www.cemac.leeds.ac.uk... Read More →
avatar for Mihaela Duta

Mihaela Duta

Research Associate and Research Software Engineer, University of Oxford
avatar for Louise Brown

Louise Brown

Senior Research Fellow, University of Nottingham
I work in the Composites Research Group in the Faculty of Engineering at the University of Nottingham. My degree was in Mechanical Engineering but I've worked as a Software Engineer both in industry and academia. I returned to academia about 10 years ago to work on the TexGen project... Read More →


Tuesday September 17, 2019 14:15 - 14:55
5. Nuffield Building, Room G17 Nuffield Building

14:30

#2A3 - Careers and Culture - "It works on my machine" - working as a research software engineer in a multi-partner international research project
When the software produced by a research project is to be re-used in several subsequent projects, it ought to be high-quality and sustainable. Yet in an heterogeneous team of researchers from several international institutions, each of them with their own background and priorities, all of them under stringent result and reporting constraints, and none of them a formally identified research software engineer, those who volunteer their time to provide quality control and run support software infrastructure are instrumental in ensuring that the team doesn't lose sight of the exigence of quality and sustainability.

In this talk, we will share our experience of taking up RSE duties in a multi-partner international space robotics project. We will give concrete examples of the technical and cultural challenges we faced, sometimes unsuccessfully. We will also briefly introduce the software engineering tools and techniques that we found worth the effort in our large-scale collaborative project, and that indeed helped with the quality and sustainability of the software, including: GitLab's collaborative and continuous integration tools, Docker containerization, unit testing, modern CMake, cppcheck and Valgrind.

Speakers
avatar for Romain Michalec

Romain Michalec

Postdoctoral Researcher, University of Strathclyde
I work on the software side of robotics and am especially interested in space and underwater applications, but my interests don't stop there. Currently involved in the nascent RSE community at my university.


Tuesday September 17, 2019 14:30 - 14:55
1. Bramall - Elgar Concert Hall Aston Webb Building

14:30

#2D3 - Revitalising Legacy Languages - Developing Fortran using Python and Literate Programming
Xcompact3d is a high-performance CFD code for simulating turbulent flows. These flows require resolving a wide range of scales for which compact finite differences are well suited with so-called ‘quasi-spectral’ accuracy, combined with a compact stencil making them computationally efficient. As part of an EPCC-funded project to implement a free-surface solver in Xcompact3d, new differencing schemes capable of resolving the discontinuous changes in field variables without introducing spurious oscillations were required, to this end a fifth-order WENO scheme was implemented.

In this talk I will present the approach followed to implement the WENO scheme, rather than write it directly in the Xcompact3d source code, it was written as a ‘literate program’. This allows the description of the program and its implementation to be interleaved, easing review and understanding of the code. Furthermore by developing it externally it was trivial to develop it as a stand-alone module which could then be wrapped with f2py to quickly test the implementation – this all implemented within the same document. Once satisfied with the implementation, the exported Fortran code could then be integrated with the Xcompact3d code base with minimal changes.

Speakers
avatar for Paul Bartholomew

Paul Bartholomew

Post-Doctoral Research Associate, Imperial College London


Tuesday September 17, 2019 14:30 - 14:55
4. Aston Webb, Room WG12 Aston Webb Building

14:30

#2B3 - Useful Tools and Libraries - GeoPandas - pepped-up Pandas for geospatial Python powers
Geospatial data pervades many areas of research, especially in the geosciences, but also in a range of spatially-rich data science applications. The Pandas Python package has provided the data science community with a flexible and powerful tool for manipulating tabular and labelled data structures. GeoPandas extends Pandas by enabling spatial operations on geometric types and providing a higher-level interface for plotting and visualising geospatial data.
This walkthrough illustrates some of the key features of GeoPandas using examples from applications at the British Geological Survey. We will demonstrate how to interact seamlessly with georeferenced databases and quickly extract and visualise data based on geographical criteria.

Speakers
avatar for Declan Valters

Declan Valters

Geoscience Software Developer, British Geological Survey

Authors
JS

John Stevenson

British Geological Survey


Tuesday September 17, 2019 14:30 - 14:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

15:00

Refreshments
Tea, coffee, water and a mini fruit scone filled with jam and cream will be provided.

Tuesday September 17, 2019 15:00 - 15:25
6. The Great Hall Aston Webb Building

15:30

Lightning Talks for Posters
A TWO minute lightning talk for each poster:
  1. N8 CIR: Building a collaborative network of RSEs across 8 northern universities: Kirsty Pringle
  2. RoboTA - an Automated Feedback and Assessment Tool: Peter Crowther
  3. RSE Enabling High Performance Computing: Anna Brown
  4. Supporting CaStLeS in the Cloud: Research Software Engineering Challenges in the Medical and Life Sciences: Simon Hartley
  5. SLURM Plugin: A Jenkins plugin for submitting jobs to SLURM systems: Eli Chadwick
  6. Developing online software for Breast and Ovarian Cancer Risk Prediction: Andrew Lee
  7. Supporting research software at Imperial College London: Jeremy Cohen, Mark Woodbridge
  8. SOMBRERO: A high-performance parallel benchmark from computational particle physics: Ed Bennett
  9. An Innovative Way to Empower Reading Notes: SN4RE: Daouda Sawadogo
  10. DYNAMO: Dynamic Analysis Modelling and Optimisation of GDI engines: Aiman Shaikh
  11. Cloud-Hosted Training on Remote Desktops: Timothy Booth
  12. Virtual Wind Tunnel: Tim Powell
  13. A journey towards Agile at scale: experiences from the SKA: Benjamin Mort
  14. Implementation and performance comparison of queuing algorithms for use in Kinetic Monte Carlo simulations: Giannis D. Savva, Michail Stamatakis
  15. Code Review tools beyond pull requests, in academia: Matthaios Alexandrakis
  16. Research vs POWER9: Keith Evans
  17. pkgreviewr: supporting rOpenSci package reviews through guidance, automation and templating: Anna Krystalli
  18. Using modern technologies to keep pace with the rapidly increasing volume of Earth Observation Satellite Data: James Dingle
  19. NAG and the RSE community: Mike Croucher


Moderators
avatar for Teri Forey

Teri Forey

Research Software Engineer, University of Leicester

Speakers
avatar for Aiman Shaikh

Aiman Shaikh

RSE, STFC
KE

Keith Evans

Senior Research Software Engineer, University of Birmingham
no
avatar for Kirsty Pringle

Kirsty Pringle

Model Domain Exper, Center for Environmental Modelling and Computation, University of Leeds
I am an atmospheric scientist and RSE, specialising in helping people use weather and climate models for research into climate change and atmospheric pollution. I work with a domain-specific technical support group called the Centre for Environmental Modelling And Computation (https://www.cemac.leeds.ac.uk... Read More →
avatar for Ed Bennett

Ed Bennett

Research Software Engineer, Swansea Academy of Advanced Computing, Swansea University
avatar for Anna Krystalli

Anna Krystalli

Research Software Engineer, University of Sheffield
avatar for Anna (Ania) Brown

Anna (Ania) Brown

RSE, University of Oxford
avatar for Peter Crowther

Peter Crowther

Research Software Engineer, University of Manchester
avatar for Simon Hartley

Simon Hartley

University of Birmingham
Talk to me about Computational Biology, Programming and Robots
EC

Eli Chadwick

Scientific Computing Graduate, Science and Technology Facilities Council
AL

Andrew Lee

Research Associate, The University of Cambridge
I work in cancer genetic epidemiology, building models to predict a person's risk of developing breast or ovarian cancer.
avatar for Daouda Sawadogo

Daouda Sawadogo

Researcher&Soft Architect, SN4RE
avatar for Timothy Booth

Timothy Booth

Developer and Bioinformatician, Edinburgh Genomics
avatar for Tim Powell

Tim Powell

Research Software Engineer, STFC Hartree Centre
I am an RSE working at STFC's supercomputing centre, the Hartree Centre.I am interested in automated workflows, coud computing, HPC, best practices, and industry collaboration.
MA

Matthaios Alexandrakis

Research Software Engineer, Queen Mary University of London


Tuesday September 17, 2019 15:30 - 16:30
1. Bramall - Elgar Concert Hall Aston Webb Building

16:30

Society of RSE Address
Moderators
Tuesday September 17, 2019 16:30 - 16:50
1. Bramall - Elgar Concert Hall Aston Webb Building

16:50

RSE Worldwide: Sharing across borders
This high profile plenary session is intended for all conference attendees.

Typically, geographic boundaries, both national and regional, can present barriers to communication and hinder the transfer of knowledge. However, RSE cuts across community and discipline borders, and covers many aspects of the research lifecycle. And so, it is very important to stimulate such knowledge transfer across these boundaries and borders.

Therefore, in this plenary session, we aim to promote the sharing of best practice in research software engineering across the various borders. In addition, we wish to prompt a discussion within selected domains about current issues and potential solutions, both during this session and hopefully afterwards on our communication channels, such as the RSE Slack workspace.

The following is an indicative agenda:

Introduction:
4.45pm – Welcome by RSE Worldwide chairs
4.50pm - A word from our session sponsor - Bradley Tipp (Microsoft) - title TBD

Keynote Talk:
4.55pm – Neil Chue Hong (ReSA) - title TBD

Lightning Talks:
5.15pm - Daniel S. Katz (US-RSE) - "US-RSE: Growing a community"
5.20pm - Stephan Druskat (DE-RSE) - title TBD
5.25pm - Niels Drost (NL-RSE) - "NL-RSE: Past, Present and Future"
5.30pm - James DesLauriers (University of Westminster, UK) - "Crossing Borders with Modularity and Microservices"
5.35pm - Sarah Gibson (Binder) - title TBD

Panel discussion:
5.40pm – Panel Q&A including invited speaker and all lightning talk speakers
6.00pm – End

Moderators
avatar for Nick May

Nick May

Software Developer (Research Data), RMIT University
avatar for Johan Philips

Johan Philips

Research Expert in Reproducible Science, KU Leuven

Speakers
avatar for Neil P. Chue Hong

Neil P. Chue Hong

Director, Software Sustainability Institute
avatar for Daniel S. Katz

Daniel S. Katz

Assistant Dir. for Scientific Software & Applications, NCSA; Research Assoc. Prof., CS, ECE, iSchool, University of Illinois Urbana-Champaign
avatar for James DesLauriers

James DesLauriers

Research Associate, University of Westminster
avatar for Stephan Druskat

Stephan Druskat

RSE, SER, PhD candidate, German Aerospace Center (DLR)
I'm a Research Software Engineer, working in linguistics, and a PhD candidate in Software Engineering at the German Aerospace Center (DLR) and the Computer Science Department at Humboldt-Universität zu Berlin in Berlin, Germany. In my work, I focus on research software sustainability... Read More →
avatar for Brad Tipp

Brad Tipp

Director Higher Education Research, Microsoft Corp
avatar for Sarah Gibson

Sarah Gibson

Research Data Scientist, The Alan Turing Institute
Among other projects, I was a core team member behind The Turing Way (https://the-turing-way.netlify.com/introduction/introduction, https://github.com/alan-turing-institute/the-turing-way) which produced a handbook to reproducible data science. I am also a mybinder team member. I'm... Read More →
avatar for Niels Drost

Niels Drost

Member of the NL-RSE Core team and Engineer at the Netherlands eScience Center, Co-PI of the eWaterCycle II project (https://www.ewatercycle.org/)


Tuesday September 17, 2019 16:50 - 18:15
1. Bramall - Elgar Concert Hall Aston Webb Building

18:25

Poster Session with drinks and nibbles
Enjoy the poster session with complimentary drinks and nibbles in the Great Hall.  A bar will also be available in the Aston Webb Foyer, accepting cash and cards.

Moderators
avatar for Teri Forey

Teri Forey

Research Software Engineer, University of Leicester

Tuesday September 17, 2019 18:25 - 19:30
6. The Great Hall Aston Webb Building

18:30

P1 - N8 CIR: Building a collaborative network of RSEs across 8 northern universities
N8 CIR is a new initiative designed to enable high impact research across the 8 northern universities in the N8 group (Leeds, Manchester, Durham, Sheffield, Liverpool, Newcastle, York, Lancaster). The centre of excellence in Computationally Intensive Research is working to identify "bottlenecks" in the research process where RSEs could use their skills, knowledge and expertise to help facilitate a wide range of research projects. Once identified, the N8 CIR will coordinate RSE effort to relieve bottlenecks. This poster will outline the community built, initial work done and reflect lessons learnt.

Speakers
avatar for Kirsty Pringle

Kirsty Pringle

Model Domain Exper, Center for Environmental Modelling and Computation, University of Leeds
I am an atmospheric scientist and RSE, specialising in helping people use weather and climate models for research into climate change and atmospheric pollution. I work with a domain-specific technical support group called the Centre for Environmental Modelling And Computation (https://www.cemac.leeds.ac.uk... Read More →


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P10 - DYNAMO: Dynamic Analysis Modelling and Optimisation of GDI engines
DYNAMO (Dynamic Analysis Modelling and Optimisation of GDI engines) is an R&D project co-sponsored by the Advanced Propulsion Centre – APC6 Call. In collaboration with Ford Motor Company (Project Lead) and six other UK based partners – Loughborough University, Bath University, Siemens CDA, Hartree Centre, Cambustion, DE&TC. The project aims to significantly improve the fuel efficiency of two high volume passenger vehicle powertrains with specific intent to simultaneously reduce CO2 and noxious emissions. Modern, fuel efficient Gasoline Direct.This has serious environmental consequences and health implications. (1). During the project the team helps to develop and mature new and upgraded advanced engine technology ready for commercialisation and aims to revolutionise the process and methodology currently used to design and develop complex powertrains. High Performance Computing (HPC) allows scientists and engineers to solve complex, compute-intensive problems efficiently. Hartree centre is supporting the project with HPC facilities and optimising the end results.
1.https://www.brookes.ac.uk/uploadedfiles/faculty_of_technology,_design_and_environment/makingthefuture.pdf

Speakers
avatar for Aiman Shaikh

Aiman Shaikh

RSE, STFC


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P11 - Cloud-Hosted Training on Remote Desktops
Edinburgh Genomics runs regular bioinformatics training courses for around twenty students at a time, often working on complex bioinformatics pipelines which require specialist software and reference data. In order to provide all participants with a full custom Linux desktop environment we now use AWS EC2 hosted instances running Ubuntu, XFCE4 and TigerVNC. After solving some initial problems and automating the setup and teardown processes we have arrived at a solution that has proved very effective and flexible. Here we share our practical experiences, lessons learned and several useful scripts.

Speakers
avatar for Timothy Booth

Timothy Booth

Developer and Bioinformatician, Edinburgh Genomics


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P12 - Virtual Wind Tunnel
The Hartree Centre is developing a Virtual Wind Tunnel (VWT) as a more cost-effective and time-saving alternative to expensive physical wind tunnel. VWT is a simulation that applies computational fluid dynamics (CFD) to a virtual design, replicating early wind tunnel tests, so the customer can proceed to a later stage in the optimisation process before the physical wind tunnel tests are needed. The Virtual Wind Tunnel is designed to bring the power of High-Performance Computing to non-HPC experts. A comprehensive workflow has been developed to build the wind tunnel environment, automate the domain decomposition, produce an automatic mesh from a 3D model file (.obj / .stl), automatically configure the CFD engine, and submit the job onto Scafell Pike. Therefore, condensing 20+ complex command lines to one simple command line, removing the complexity of a virtual wind tunnel simulation for a non-technical user, but still running the same high-quality simulation.

Speakers
avatar for Tim Powell

Tim Powell

Research Software Engineer, STFC Hartree Centre
I am an RSE working at STFC's supercomputing centre, the Hartree Centre.I am interested in automated workflows, coud computing, HPC, best practices, and industry collaboration.


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P13 - A journey towards Agile at scale: experiences from the SKA
The Square Kilometre Array (SKA) project is an international effort to build the world’s largest radio telescope. Unlike traditional radio telescopes the SKA will be defined largely by its software. Production is expected to start next year and will involve well over 100 developers working together to deliver a complex system consisting of everything from control systems to high throughput signal processing to science pipelines running on cloud-like infrastructure. The challenge of managing and organising this effort to a single purpose, and delivering the telescope on time and budget is considerable. To make this achievable, the SKA has adopted the Scale Agile Framework and is currently working towards putting this into practice. While more commonly used for large software projects in industry, this is a rather novel approach for the astronomical community. In this poster we will introduce the approach being taken and the tools being used to implement it for the SKA project.

Speakers

Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P14 - Implementation and performance comparison of queuing algorithms for use in Kinetic Monte Carlo simulations
Zacros (http://zacros.org) is a Graph-Theoretical Kinetic Monte Carlo software application for simulating molecular phenomena on catalytic surfaces. The implemented method for listing and randomly choosing a process is based on the idea that the next event to occur has to be the one with the smallest waiting time. The main task is, therefore, reduced to creating a “catalogue” containing the waiting time of all realizable events, finding their minimum and updating the time values of the involved processes.
A Skip List based data structure was implemented in Zacros and further extended to provide us with an almost constant time removal operation. Benchmarks have shown that the new algorithm outperforms the existing one, the “Binary Heap”, in a special class of problems. The “bottlenecks”, namely the operations that potentially hinder performance were clearly identified and discussed along with possible performance improvements.


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P15 - Code Review tools beyond pull requests, in academia
Industry relies on code review to increase quality of submitted code. In academia, code review is more rarely used for a variety of reasons. A significant portion of code review in both cases takes part inside Github pull requests.

Industry's regular production cadence demands focus on post-commit and pull request reviews, while review performance metrics become relevant enough to be tracked.

In research software development the scope is different. Metrics are unimportant. Codebases under development can take advantage of commit reviews, a feature readily available in Github. However, when dealing with developed or legacy codebases, pre-commit reviews become just as important when extensive code marking is required. In addition, academic users' skill variance is much larger than in the software developer community, and has to be taken into consideration when a choice for a tool is made.

The different problems of scientific software development require an altered approach. Are there cases where pull requests are insufficient? This poster presents an exploration of code review tools for academic research software development.

Speakers
MA

Matthaios Alexandrakis

Research Software Engineer, Queen Mary University of London


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P16 - Research vs POWER9
It is difficult to argue against the dominance of Intel CPU architecture for HPC over the last decade. It is equally difficult to argue against the growing interesting in AI, Machine learning (ML) and Deep Learning (DL) for which such architectures are not optimised. Enter on to the scene, NVIDIA with tesla GPUs and tensor cores designed for fast matrix-matrix multiplications, ideal for AI, ML and DL. However, one drawback, memory; even the largest GPUs only have 32Gb which can be a limiting factor on the research problems which can be tackled. Using the mainboard RAM isn’t a solution to this issue due to the low bandwidth of the PCIe ports through which GPUs are normally attached to the system; but what if that issue was solved? Connect the GPU to the mainboard RAM via a high bandwidth interconnect and allow the GPU to access feasibly Tbs of RAM; this is the ethos of the POWER9 infrastructure from IBM. The University of Birmingham has now entered into a strategic partnership with IBM and is home to the largest POWER9 cluster in the UK with 11 nodes and a whopping 44 Tesla GPUs. With a year of use, we here will here present preliminary results of several case studies which take advantage of the POWER9 architecture.

Speakers
KE

Keith Evans

Senior Research Software Engineer, University of Birmingham
no


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P17 - pkgreviewr: supporting rOpenSci package reviews through guidance, automation and templating
The R research community has been extremely fortunate for the existence of rOpenSci. (https://ropensci.org/). rOpenSci curate an impressive collection of community contributed packages to support open reproducible research and data access in R. The peer review system used has not only improved the quality of contributed packages, but the practice of reviewing itself has elevated the skills of the whole community involved, by engaging us with best practice. The key to this success is a formalised review process based on detailed recommendations and guidelines (https://ropensci.github.io/dev_guide/). To help reviewers further, rOpenSci have also focused on tooling and automation. One such tool is pkgreviewr (https://github.com/ropenscilabs/pkgreviewr), an R package that helps automate some of the steps and guide reviewers through the review process. In this poster I’ll present an overview of the rOpenSci review process and the use of pkgreviewr to support it. I’ll also tell the story of how the package came to be and how such contributions can lead to deeper involvement with the community.

Speakers
avatar for Anna Krystalli

Anna Krystalli

Research Software Engineer, University of Sheffield


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P18 - Using modern technologies to keep pace with the rapidly increasing volume of Earth Observation Satellite Data.
The launch of the ESA Sentinel 3A and 3B satellites providing 300m global ocean colour data present new opportunities to observe finer scale oceanographic features. However, the satellites represent a 20-fold increase in data volumes compared to earlier sensors and, hence, a significant computational challenge using existing processing tools. In this poster, we share our experience of reducing bottlenecks in satellite data processing workflows and expand upon the use of new technologies such as xarray and dask to address these. As an example, we present how an updated ocean-colour processing chain has been incorporated into our operational processing systems to allow processing over 1.1 billion pixels per day as part of the ESA funded project: Earth Observation for Sustainable Development (EO4SD).

Speakers

Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P19 - NAG and the RSE community
Almost 50 years ago, The Numerical Algorithms Group (NAG) was formed from a collaboration between the Universities of Birmingham, Leeds, Manchester, Nottingham and Oxford. Its aim was, and still is, to improve computational research by improving the quality of the numerical libraries on which such research critically depends.  You could argue that NAG was the first sustainable RSE group.   Fast forward to 2019 and NAG remains close to its academic roots in many areas. We are industrial partners on international grants, collaborate with research groups across the UK, accept undergraduate industrial placement students, support Centres for Doctoral Training, fund PhD students and much more. Additionally, many universities around the UK have full site licenses for many of NAG's products and service contracts to provide training and support. This poster explores some of the RSE-related projects we are currently working on with our academic collaborators.

Please note that this poster is not part of the poster competition.

Speakers

Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P2 - RoboTA - an Automated Feedback and Assessment Tool
Giving individual feedback to students while teaching is an important part of their development and learning. However, the level of feedback given to students is often limited by the availability of time and resources. RoboTA is an automated tool to provide continuous feedback and assessment for student coursework. As students submit partial versions of coursework, RoboTA evaluates the students’ progress and provides feedback, including early detection of common mistakes and best practice compliance. In addition, a student performance dashboard has been developed to assist teaching assistants in rapidly assessing student and team performance throughout the course. The tool is modular in its construction which means it should be easy to extend in the future. RoboTA is currently being developed for an undergraduate course in Software Engineering, in the future we plan to extend its functionality to a wider range of courses in Computer Science and potentially further into other departments. RoboTA is one strand of the Institute of Coding (IoC) work we are doing at the University of Manchester. The IoC is a consortium of universities and employers developing the next generation of digital talent at degree level and above.

Speakers
avatar for Peter Crowther

Peter Crowther

Research Software Engineer, University of Manchester


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P3 - RSE Enabling High Performance Computing
Modern HPC systems are often heterogeneous and massively parallel, leading to highly complex codes which take significant effort to maintain and test. In addition, specialised expertise in profiling and optimisation for a particular target architecture is often required to get close to the peak theoretical performance. Researchers are not guaranteed to have received software development or HPC training, and don't necessarily have the time to spend on software maintenance.

Speakers
avatar for Anna (Ania) Brown

Anna (Ania) Brown

RSE, University of Oxford


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P4 - Supporting CaStLeS in the Cloud: Research Software Engineering Challenges in the Medical and Life Sciences
We are working with the new world of data driven research. Few fields have had the explosive change and adoption of big data, AI and HPC systems as much as medical and life science research. This shown by the universities recent Advanced Research Computing (ARC) and Compute and Storage for Life and environmental Sciences (CaStLeS) initiatives. The challenges faced by researchers in this field are varied. They range from scripting and programming tasks, for file format conversions to the data intensive tasks such as bioinformaticians annotations of mouse embryo gene-expression databases, to computational intensive tasks such as genomics whole genome sequence analysis, to the emerging AI fields such as computer vision for MRI scans. If this seems challenging for the researchers it is more so for research software engineers (RSE’s) in this field who have to support them via specialist knowledge in programming, secure and reliable data management, AI, statistics.

Speakers
avatar for Simon Hartley

Simon Hartley

University of Birmingham
Talk to me about Computational Biology, Programming and Robots


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P5 - SLURM Plugin: A Jenkins plugin for submitting jobs to SLURM systems
This poster will present a Jenkins plugin, developed on Anvil (https://anvil.softeng-support.ac.uk/), which allows HPC jobs to be run on SLURM systems through the Jenkins interface. Tools such as Jenkins facilitate automation of tests through continuous integration, but do not currently suit the needs of developers who want to test their software on HPC systems - this plugin aims to resolve this issue. I will share how the plugin can be used, and discuss the potential for extension to other batch systems.

Speakers
EC

Eli Chadwick

Scientific Computing Graduate, Science and Technology Facilities Council


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P6 - Developing online software for Breast and Ovarian Cancer Risk Prediction
Breast cancer (BC) is the most common cancer in UK females, with about 1 in 8 developing it. Ovarian cancer (OC), although less prevalent, has worse survival rates as it is often not diagnosed until an advanced stage. For both, survival rates increase with earlier diagnosis. Risk models allow identification of women at highest and lowest risk, and so those most likely to benefit from alternative screening modalities and/or preventative treatments. BC and OC risks are multifactorial, depending on genetic, family history and other lifestyle/hormonal/reproductive risk factors. We have developed comprehensive BC (BOADICEA) and OC risk models. As risk prediction is computationally intensive, they have been optimised for real-time clinical use. The models will be accessible for clinical use via a new online tool (www.canrisk.org), developed by a team of software developers, clinicians and scientists following a standard framework and using established software engineering practices. Since such tools are classified as medical devices they must adhere to medical device regulations for safety, quality and efficacy (CE marking). We are currently undertaking the necessary additional risk/quality management and software engineering work.

Speakers
AL

Andrew Lee

Research Associate, The University of Cambridge
I work in cancer genetic epidemiology, building models to predict a person's risk of developing breast or ovarian cancer.


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P7 - Supporting research software at Imperial College London
The wide range of RSE teams that have been set up at institutions across the UK and internationally demonstrates the growing importance of research software engineering and how it is now considered to be a key aspect of the research environment. However, providing RSE capabilities at an institution is not only about setting up an RSE team. The wider research community and the many researcher/developers who are likely to remain within research groups are also important in ensuring sustainable, reliable and robust research software outputs. In this poster we will present our RSE activities at Imperial College London that cover research software development, a research software community and a programme of training workshops that are helping to develop the next generation of research software developers. We consider that this set of different activities offers a complete package to support research software and ensure strong and reproducible research outputs. It also has the potential to act as a template or case study for other institutions looking to bring together similar sets of RSE capabilities. The poster will include a group of co-authors representing the different RSE activity areas.


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P8 - SOMBRERO: A high-performance parallel benchmark from computational particle physics
SOMBRERO is a high-performance parallel HPC benchmark developed from research software used in Lattice Gauge Theory. SOMBRERO specifically tests the conjugate gradient inversion of a physically interesting sparse stencil operator across a four-dimensional array of small complex matrices. Since the shape of these matrices and the vectors on which they act changes with the properties of the theory under study, so does the ratio of floating point computations to the number of bytes sent across the interconnect. The benchmark has been tested on a variety of platforms and architectures, including Intel, AMD, and Arm microarchitectures and Intel and Mellanox interconnects. In this poster, we will present details of the operation of the benchmark, and test results from a sample of systems we have tested.

Speakers
avatar for Ed Bennett

Ed Bennett

Research Software Engineer, Swansea Academy of Advanced Computing, Swansea University


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

18:30

P9 - An Innovative Way to Empower Reading Notes: SN4RE
A researcher reads an average of 22 papers per month and has spent an average of 48 minutes on each paper. Sometimes, we can only experience several hours of deep reading mode, but SN4RE is designed to empower us by helping researchers to manage their reading notes on a well-structured note format (Smart Notes for Research). This platform helps researchers to grasp the essential information of a given paper and provides the opportunities to share aspects of readings that could help other researchers understand their research papers, while saving time in getting a consistent overview. It prevents the rereading of the same paper over again, by providing a concise summary of their reading, SN4RE is a Responsive Platform with numerous features to empower your reading notes.

Speakers
avatar for Daouda Sawadogo

Daouda Sawadogo

Researcher&Soft Architect, SN4RE


Tuesday September 17, 2019 18:30 - 19:30
6. The Great Hall Aston Webb Building

19:30

Buffet conference dinner (for all attendees, no ticket needed) sponsored by Oracle
A hot fork buffet will be provided from 8pm. Menu tbc soon.


Tuesday September 17, 2019 19:30 - 21:30
6. The Great Hall Aston Webb Building
 
Wednesday, September 18
 

08:30

Registration (Foyer)
If you're just joining the conference on day 2 then please register and pick up your badge etc. from the registration desk.

Tea, coffee and water will be avaialble from 8:30 am in the Great Hall.

In the Aston Webb Building near to the registration/reception desk, a cloakroom is available in room G30 along with a quiet room in G31.

Wednesday September 18, 2019 08:30 - 09:00
6. The Great Hall Aston Webb Building

09:00

Welcome
Moderators
avatar for Andrew Edmondson

Andrew Edmondson

Research Software Group Leader, University of Birmingham
I'm a research software engineer, theologian and mathematician. I am the Programme Chair of RSEConUK 2019 and chair of the Power AI User Group.

Wednesday September 18, 2019 09:00 - 09:10
1. Bramall - Elgar Concert Hall Aston Webb Building

09:00

Posters available to view from 9am to 5pm
Wednesday September 18, 2019 09:00 - 17:00
10. Mezzanine Floor, (First floor), Bramall Foyer Bramall Elgar Concert Hall, Above Costa coffee

09:10

Lightning talks for DAY 3 Workshops
Come and hear a lightning talk for each workshop tomorrow (DAY 3) to help you choose which workshops to attend

Moderators
avatar for Roland Guichard

Roland Guichard

Research Software Engineer, University College London

Speakers
avatar for Andrew Laidlaw

Andrew Laidlaw

AI Infrastructure Specialist, IBM
avatar for Tania Allard

Tania Allard

RSE conference diversity and accessibility chair, Microsoft
PR

Phil Ridley

Staff Field Applications Engineer, Arm
avatar for Diego Alonso Álvarez

Diego Alonso Álvarez

Research Software Engineer, Imperial College London
avatar for Sarah Gibson

Sarah Gibson

Research Data Scientist, The Alan Turing Institute
Among other projects, I was a core team member behind The Turing Way (https://the-turing-way.netlify.com/introduction/introduction, https://github.com/alan-turing-institute/the-turing-way) which produced a handbook to reproducible data science. I am also a mybinder team member. I'm... Read More →
avatar for Fergus Cooper

Fergus Cooper

Research Software Engineer, University of Oxford
I am currently working as a research software engineer at the University of Oxford, having helped found the Oxford RSE group in December 2018. Since then, the group has more than doubled in size, and we’re looking forward to collaborating with the UK RSE community and with the open... Read More →
avatar for Andres-Leonardo Martinez-Ortiz

Andres-Leonardo Martinez-Ortiz

Google
Andres-Leonardo Martinez-Ortiz a.k.a almo is a member of the Google Engineering team, leading Google Cloud Ecosystem program in Europe. Based in Zurich, he drives the success of Google's developer products and the Open Web by creating a thriving ecosystem of developers. He meets with... Read More →


Wednesday September 18, 2019 09:10 - 09:25
1. Bramall - Elgar Concert Hall Aston Webb Building

09:30

#3A1 - Citation and Software Discovery - How to learn which software is developed in your institution?
I will present the Code4REF project (https://code4ref.github.io/) which aims at providing guidelines on recording research software in CRIS (Current Research Information Systems). Many universities use CRIS to record research publications, e.g. to display them on their webpages and, in the UK, for preparing submissions for REF (Research Excellence Framework) and reporting research outputs to funding bodies, while software outputs are much less common there.

We believe that scientific code needs to be treated as a primary research output, and should be equally well covered by CRIS. This will not only be useful for the above mentioned purposes, but will allow e.g. to get an overview of all research software developed at an institution, in the research group or by an individual developer using CRIS or their public views. This will provide further evidence that software is vital for research, and will contribute to the campaign for the recognition of the RSE role within academia.

I will outline the current state of the project, explain how you can contribute by providing guidance to further CRIS and promoting Code4REF in your institutions. I will also outline the vision of further grassroots campaign which starts from Code4REF.


Wednesday September 18, 2019 09:30 - 09:55
1. Bramall - Elgar Concert Hall Aston Webb Building

09:30

#3C1 - Design Methodologies and Project Planning - Cheap, fast, or secure? When research projects meet real-world participants
It is often said that the 'S' in IoT stands for security. In a similar vein, the 'P' in the name might be said to stand for privacy-first design. There is a large and challenging gap between functional adequacy and best practice.

In this talk, we describe the process of developing the 'home gateway' for the SPHERE 100-homes project, a Linux-based research data aggregator installed into participant homes around Bristol in order to act as an endpoint for healthcare data collection on human participants.

We begin by briefly describing the regulatory landscape that applies to human-centred research data. We tested and used open-source packages and services designed to fill as many gaps in our service design as possible. We also had to find solutions for the further, specific challenges raised by the particular requirements of the project, such as data encryption at rest, robust behaviour in the face of unexpected input or events, and auditable data workflows. Finally, we look at the everyday challenges of safely and securely maintaining a sustainable platform in the face of the risks posed by real-world vulnerabilities - patching, system updates and responding to new flaws discovered in standards, hardware and firmware.

Speakers
avatar for Gregory J. L. Tourte

Gregory J. L. Tourte

The University of Bristol


Wednesday September 18, 2019 09:30 - 09:55
5. Nuffield Building, Room G17 Nuffield Building

09:30

#3D1 - Machine Learning - Pushing the Limits of Exoplanet Discovery via Direct Imaging with Deep Learning
One technique to detect these distant worlds is through the direct detection of their thermal emission. The so-called direct imaging technique is suitable for observing young planets far from their star.

Due to the star emissions, these are very low signal-to-noise-ratio (SNR) measurements. Moreover, the limited and highly unbalanced ground truth hinders the use of supervised learning approaches to automatically detect planets signals in the images.

In this talk, we show how to bypass the scarcity of real data by training a Generative Adversarial Network. The synthetic images produced by the generative model can be assumed to not contain any planet and are augmented by artificially injecting planets signals. The data obtained are not just labeled but, for the positive samples, the exact position of the object to detect is known. CNN detectors trained on this synthetic dataset exhibit good predictive performance and, on real data, the models can re-confirm bright sources detection. In this sense, the above technique seems to go beyond the current state of the art in exoplanet discovery via direct imaging.

Speakers

Wednesday September 18, 2019 09:30 - 09:55
4. Aston Webb, Room WG12 Aston Webb Building

09:30

#3B1 - HPC and Novel Clusters - Getting Started on an Arm HPC System
Arm processor based HPC platforms are now available. In the UK there is Isambard (Cray XC50) and three Catalyst (HPE Apollo 70) systems. These systems are supported by Arm’s extensive HPC ecosystem, which means that most applications will build with little or no modification, furthermore it usually takes little effort to achieve maximum performance out of your application on Arm. The main objective of this walkthrough is to demonstrate how easy it is to use Arm HPC systems to do real science. The session will begin with an overview of Arm in HPC, Isambard and Catalyst. Then, a more in-depth demonstration of some of the tools that are available. This will include compilers, numerical libraries, debugging tools and profiling tools. The demonstration will end with a discussion of some recent results from Isambard and Catalyst. Throughout the walkthrough there will be opportunity to discuss how to get best performance with your application or to use the tools, and to ask any questions in general about Arm in HPC.

Speakers
PR

Phil Ridley

Staff Field Applications Engineer, Arm


Wednesday September 18, 2019 09:30 - 09:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

10:00

#3A2 - Citation and Software Discovery - Building a network of connected research
The persistent identifier community is an academic-tangential tech community much like the research software engineers. (Some of us are even the same people!) We're trying to make sure that researchers, the stuff they do, and the tools they work with are identified in ways that are unique, persistent, and make sense to machines. We envision a future where there's a network of these identifiers tracing which articles were written by which people using which datasets and software, and so on. But what good is a network if no one is using it? You're invited to contribute to the movement, whether through open software development, or just by being opinionated about interconnected research. This talk will give you a high-level view of persistent identifiers, who's using them and why, and tools you can use now in your own research software endeavors.

Speakers

Wednesday September 18, 2019 10:00 - 10:25
1. Bramall - Elgar Concert Hall Aston Webb Building

10:00

#3C2 - Design Methodologies and Project Planning - Retrofiting research software engineering practices to active research tools
Researchers often develop their own tools to facilitate their work and support the publication process. In very rare cases, some of them will make the additional effort to make these tools available to the whole research group or even to researchers across institutions. However in most cases these tools tend to evolve and morph organically over time, following the immediate needs of the researcher. Questions like data management and sustainable data preservation practices are usually left to the future.

In this talk I will present the challenges of joining such a research group, BRIDGE, and slowly moving from an adhoc environment to a mostly fully managed full stack system. Our research involves climate modelling, past, present and future, generating many TBs of data weekly that requires storage, analysis, visualisation, availability for reuse, and eventual archiving. Working towards a managed, sustainable outcome required close integration with University systems.

By effective collaboration, we built a home grown processing suite used to manage, process, analyse and share data, capable of scaling up to suit our full dataset, likely to exceed petabyte scale in the next few years. This suite is also used for teaching purposes.

Speakers
avatar for Gregory J. L. Tourte

Gregory J. L. Tourte

The University of Bristol


Wednesday September 18, 2019 10:00 - 10:25
5. Nuffield Building, Room G17 Nuffield Building

10:00

#3D2 - Machine Learning - The Limitations of Machine Learning
Machine Learning (ML) is a popular topic in the research world. It has spread from basic computer science research to many other disciplines and RSEs are increasingly encouraged to be familiar with applying it to their projects.

In this talk I will discuss various limitations of ML, including how it can augment human bias, the problem with interpreting complex deep learning models and how real-world data can harm your model.

I'll end with some tips on how to tell if using ML is even the right solution for your project, and some alternatives for if it's not.

Speakers
avatar for Camilla Longden

Camilla Longden

Research Software Engineer, Microsoft Research
I'm an RSE at Microsoft Research in Cambridge. I work in the Deep Learning Engineering team in the ADA (All Data AI) group. I am also interested in diversity and inclusion in the technology sector.


Wednesday September 18, 2019 10:00 - 10:25
4. Aston Webb, Room WG12 Aston Webb Building

10:00

#3B2 - HPC and Novel Clusters - Zero to Cluster in 20 Minutes: There and Back Again
Find out how you can create a cluster in the cloud and run your analysis on it in less then twenty minutes. We'll go through the process of allocating cloud resources to create an auto-scaling, heterogeneous compute cluster with a clustered filesystem and a software stack with a familiar HPC-style interface and finally destroy the whole thing, all for about 30 pence.

Speakers
avatar for Matt Williams

Matt Williams

Research Software Engineer, University of Bristol
Matt works at the University of Bristol in the JGI as a Research Software Engineer. Matt joined the University in 2016, coming from the University of Birmingham where he provided support for the LHC's world-wide computing platform. He worked to support the synthetic biology community... Read More →


Wednesday September 18, 2019 10:00 - 10:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building

10:30

#3A3 - Citation and Software Discovery - How to make software fit in the research citation graph
References between research products (papers, monographs, software, data, etc.) provide context, inform about predecessors and precedents, and make it possible to trace citation, which in turn provides credit for researchers and institutions. Together, research products, researchers, institutions, and the relations between them form a graph, a "research citation graph". With the increasing awareness of the importance of software for research, and ongoing efforts to make citation work for software, I look at modeling software and its specific properties into this kind of graph, which has traditionally been used for text-based publications only. In this talk, I propose some changes that need to be made to fit software and their dependencies into a citation graph. These changes pertain to differences across types of research product, and concepts specific to software. I will suggest how to implement these changes for a citation system which is better suitable for providing fair credit for research software than what we have right now. And finally, I will give an outlook on future work on automatically retrieving citation graphs for software, and weighting relations in them.

Speakers
avatar for Stephan Druskat

Stephan Druskat

RSE, SER, PhD candidate, German Aerospace Center (DLR)
I'm a Research Software Engineer, working in linguistics, and a PhD candidate in Software Engineering at the German Aerospace Center (DLR) and the Computer Science Department at Humboldt-Universität zu Berlin in Berlin, Germany. In my work, I focus on research software sustainability... Read More →


Wednesday September 18, 2019 10:30 - 10:55
1. Bramall - Elgar Concert Hall Aston Webb Building

10:30

#3C3 - Design Methodologies and Project Planning - Got agility? A lightweight technique for Productivity Sustainability Improvement Planning (PSIP)
PSIP (Productivity Sustainability Improvement Planning) is a lightweight, iterative workflow where teams identify their most urgent software bottlenecks, and track progress on work to overcome them. PSIP captures the tacit, more subjective aspects of team collaboration, workflow planning, and progress tracking. In the potential absence of appropriate planning PSIP is designed to bootstrap small, large, and loosely-coupled aggregate team capabilities into best practices, and encourage teams to adopt a culture of process improvement. In this talk we highlight the PSIP stories of two exascale scientific software teams, Exascale Atomistic capability for Accuracy, Length and Time (EXAALT), and Exascale MPI (Message Passing Interface) MPICH (High Performance Message Passing Interface). The EXAALT team used PSIP to adopt continuous integration practices. MPICH focuses on developing a production-ready high-performance MPI implementation that scales to supercomputers. MPICH used PSIP to develop tools for onboarding new team members. In discussing the strengths and weaknesses of the PSIP process in use with these and other research science software teams we will discuss why PSIP helps teams mitigate technical risk.

Speakers
avatar for Elaine M. Raybourn

Elaine M. Raybourn

Principal Member of the Technical Staff, Applied Cognitive Science, Sandia National Laboratories


Wednesday September 18, 2019 10:30 - 10:55
5. Nuffield Building, Room G17 Nuffield Building

10:30

#3D3 - Machine Learning - Investigating Deep Learning Approaches for Robust Zooplankton Identification
Plankton support the marine ecosystem & are extremely sensitive to environmental change. The Marine Biological Association of the UK have been exploring new, autonomous imaging technology for rapid estimation of zooplankton abundance in order to improve monitoring & reporting speed to meet legislative monitoring requirements. In collaboration with EPCC, development of robust, automated plankton classification systems are being explored. The Continuous Plankton Recorder Survey has been used to generate an image dataset of zooplankton species generated via a digital imaging system; this project outlines the development, training & validation of Convolutional Neural Networks (CNN) on highly imbalanced datasets for rapid classification. Using a ready-labelled training dataset of 20 zooplankton species, a number of architectures & ensemble methods have been explored to obtain high accuracy classification; robust strategies for handling extreme class imbalance have been developed such that species that occur very infrequently & in low numbers can be reliably classified in near real-time. By optimising the CNNs for use on GPUs on EPCC’s CIRRUS HPC system, we will show how we have improved on existing work in this rapidly evolving field.

Speakers
avatar for Chris Wood

Chris Wood

Applications Consultant, EPCC, University of Edinburgh

Authors

Wednesday September 18, 2019 10:30 - 10:55
4. Aston Webb, Room WG12 Aston Webb Building

10:30

#3B3 - HPC and Novel Clusters - Running simulations on a massively-parallel low-power machine
SpiNNaker is a massively parallel low power supercomputer designed to model large spiking neural networks in real time, consisting of 1 million ARM cores, each with a low instructional memory (ITCM) limit of 32K. The architectural design of the machine lends itself easily to the simulation of spiking neural networks due to its ability to send and route multiple small messages from any point on the machine to multiple other points simultaneously. It has also been used for other massively-parallel simulations.

This walkthrough will demonstrate some of the features of different applications and scripts that can be run on the machine, including the link-up with the EU Human Brain Project's Neurorobotics Platform. It will also demonstrate some of the ways that the software team runs workshops and troubleshoots problems for both new and existing users, via for example Jupyter notebooks and lab manuals.

Speakers
avatar for Andrew Gait

Andrew Gait

Research Software Engineer, University of Manchester


Wednesday September 18, 2019 10:30 - 10:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

11:00

Refreshments
Tea, coffee,  water and biscuits will be provided in the Great Hall.

Wednesday September 18, 2019 11:00 - 11:25
6. The Great Hall Aston Webb Building

11:30

Keynote: Bad Science/Wrong Number
Have you ever wondered how one day the media can assert that alcohol is bad for us and the next unashamedly run a story touting the benefits of daily alcohol consumption? Or how a drug that is pulled off the market for causing heart attacks ever got approved in the first place? How can average people, who aren’t medical doctors or Ph.D.s in biochemistry, tell what they should be paying attention to and what’s, well, just more bullshit?
Ben Goldacre has made a point of exposing quack doctors and nutritionists, bogus credentialing programs, and biased scientific studies. But he has also taken the media to task for its willingness to throw facts and proof out the window in its quest to sell more copies.
But he’s not here just to tell you what’s wrong. Goldacre is here to teach you how to recognise bad science when you see it. You’re about to feel a whole lot better.

Speakers
avatar for Ben Goldacre

Ben Goldacre

Ben Goldacre is an award-winning writer, broadcaster, doctor, academic and campaigner who specialises in unpicking scientific claims made by scaremongering journalists, government reports, pharmaceutical corporations, PR companies and quacks. He trained in medicine at Oxford and UCL... Read More →


Wednesday September 18, 2019 11:30 - 12:25
1. Bramall - Elgar Concert Hall Aston Webb Building

12:30

Lunch and poster prize awards
A cold fork buffet will be provided in the Great Hall. Menu tbc.

Wednesday September 18, 2019 12:30 - 13:25
6. The Great Hall Aston Webb Building

13:30

#4A1 - Community and Collaboration - Research Software Engineering in Jordan - The MaDiH (مديح) Project
MaDiH (مديح) involves King’s Digital Lab (KDL) / King's College London eResearch, the Hashemite University, the Council for British Research in the Levant (CBRL), the Department of Antiquities of Jordan, the Jordanian Open Source Association, and the EAMENA project. The project delivers training in Research Software Engineering (RSE) best practice, alongside white papers, a prototype National Data Catalogue, and a prototype National Heritage Portal. Workshops are identifying datasets, held both in Jordan and overseas, to ‘repatriate’ (through federation) data collected in Jordan but held offshore. The project is contributing to the development of Jordan’s digital cultural heritage, identifying key systems, datasets, standards, and policies, and aligning them to government digital infrastructure capabilities and strategies. By defining a robust architecture for digital cultural heritage, informed by RSE best practice, the aim is to assist the Department of Antiquities in their planning processes, help product development teams develop their systems, facilitate the aggregation of valuable datasets held in disparate repositories, and ensure data generated from research activity is properly stored and widely accessible.

Speakers
avatar for James Smithies

James Smithies

Director, King's Digital Lab, King's College London
I'm director of King's Digital Lab, a software engineering team specialising in arts & humanities and social science research. I am also Deputy Director of eResearch for King's College London.

Authors
AZ

Andrea Zerbini

Council For British Research in the Levant
CP

Carol Palmer

Council For British Research in the Levant
FB

Fadi Bala'awi

Hashemite University
PF

Pascal Flohr

University of Oxford
SI

Sahar Idwan

Hashemite University
SR

Shaher Rababeh

Hashemite University


Wednesday September 18, 2019 13:30 - 13:55
1. Bramall - Elgar Concert Hall Aston Webb Building

13:30

#4D1 - Cloud Technologies and Case Studies - Case study of porting a pipeline to EMBL-EBI Cloud Portal
Case Study of Porting a Bioinformatics Pipeline into Clouds

Cloud providers have different UIs, architectures and APIs. For the research community, it is extremely important to be cloud-agnostic while enjoying advantages of different clouds. It is also extremely important to make the cloud technologies easily accessible for lab scientists with little to no training in clouds. Kubernetes and Docker as a de facto standard is making such goals closer to reality.

We ported a legacy pipeline from a bare-metal LSF-based stack to Kubernetes on OpenStack. With minimal changes to the pipeline itself, but by using cloud features intelligently we have made major improvements, changing the pipeline from a single-user local application to a shared multi-user application accessible over the Internet. To investigate and to confirm the cloud-agnostic nature of our solution, we created a CI/CD toolchain to deploy the pipeline onto Kubernetes clusters created on all four major clouds: Google, Amazon, Microsoft and OpenStack. The pipeline can run consistently on GKE, EKS, AKS and EHK, where EHK is the Kubernetes service at European Bioinformatics Institute for research teams to request clusters from.

The general solution that we have developed provides a common set of programming interfaces to support major cloud providers in a consistent, agnostic manner. This reduces the learning curve and skill requirements to port and deploy pipelines in the clouds. This talk presents the methods and the lessons learned during the exercise. It demonstrates the feasibility to rejuvenate legacy pipelines in the clouds with minimum effort.

Speakers
avatar for David Yuan

David Yuan

Cloud Bioinformatics Application Architect, European Bioinformatics Institute
David Yuan is a Cloud Bioinformatics Application Architect working at European Bioinformatics Institute (EBI), European Molecular Biology Laboratory (EMBL). He is driving cloud-adoption onto both private cloud (OpenStack) and public clouds (Google Cloud Platform, Amazon Web Services... Read More →


Wednesday September 18, 2019 13:30 - 13:55
4. Aston Webb, Room WG12 Aston Webb Building

13:30

#4B1 - Training, Teaching and Code Review - Nbfancy: Generating and delivering better training material
The walkthrough will introduce NBfancy, a library to enrich Jupyter notebook content, and demonstrate its simple workflow to create/modify teaching material. Developing tutorials for programming often proceeds as follows: 1. Start document 2. While (not finished): a Write narrative b Write perfect example code c Run code d Copy code to document e Copy output to document 3. Write slides/handouts/exercises As we work, we notice mistakes, or find a better way of writing earlier examples. We go back, change the code and copy/paste the new input and output, which makes creating or updating training material time-consuming and undesirable. Jupyter notebooks go some way to fix this, with narrative in markdown, with basic formatting alongside code and with output in the same document. We also like the Software Carpentry (SC) teaching material, but recreating the look and practice it embraces in notebooks is not trivial. NBfancy is developed to combine the flexibility of notebooks and include SC’s pedagogy. NBfancy is a set of tools written to augment notebooks, allowing you to develop training material more effectively. We will illustrate its use with an overview of the library and some of our teaching materials.

Speakers
avatar for James Grant

James Grant

Research Software Engineer, University of Bath


Wednesday September 18, 2019 13:30 - 13:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

13:30

#4C1 - Institutional Support for RSEs - Supporting RSEs at the Science and Engineering South universities and across the UK
Science and Engineering South (SES) is a consortium of six major universities based in the South East that have an excellent history of supporting the RSE community. The RSE campaign was led from the University of Southampton, UCL developed the model for the RSE Group which has spread across the country, and all the participating universities support RSE activities.

Our panel will bring together at least one of the Pro-Vice Chancellors from the SES universities (potentially two, dependent on scheduling of the panel), heads of RSE Groups within SES, a senior university HR representative and a representative from the Society of RSE.

Over the last six months there has been a drive by the SES universities to recognise the RSE career path. The panel will discuss why SES universities are choosing to increase support for RSEs, the problems that have held back recognition for RSEs and the SES institutions’ approach to solving them. The goal of the panel is to support the growth of RSE careers across UK academia by sharing the experiences of the SES institutions in supporting RSEs.

Speakers
avatar for Simon Hettrick

Simon Hettrick

The Software Sustainability Institute
I've been involved with RSEs since the beginning of the RSE campaign in 2013, so I'm always happy to talk about RSE activities and history. I have a strong interest is software use and in understanding more about the demographics of researchers who rely on software.


Wednesday September 18, 2019 13:30 - 14:25
5. Nuffield Building, Room G17 Nuffield Building

14:00

#4A2 - Community and Collaboration - The Setup of an Institute for Scientific Software, connecting Applied Computing and Data Intensive Sciences
With the ever increasing size of scientific collaborations and complexity of scientific instruments the software needed to acquire, process and analyze the gathered data is gaining in complexity and size too. Unfortunately the role and career path of scientists and engineers working on software R&D and developing scientific software is neither clearly established nor defined in many fields of natural science. In addition the exchange of information between scientific software development and computer science departments at universities or computing schools is scattered and de-fragmented into individual initiatives. To address the above issues we propose an effort on an European level, which concentrates on strengthening the role of software developers in natural sciences, acts as a hub for exchange of ideas among different stakeholders in computer science and scientific software and forms a lobbying forum for software engineering in natural sciences on an international level. This contribution discusses in detail the motivation, role and interplay with other initiatives of a "Software Institute for Data Intensive Science" which is currently being discussed.

Speakers
avatar for Stefan Roiser

Stefan Roiser

Senior Computing Engineer, CERN
I am a computing engineer in the IT department at CERN, Switzerland. My main interest is on data processing software frameworks and applications in high energy physics and their evolution in an evolving hardware landscape. Furthermore I am also interested in the possibility to establish... Read More →


Wednesday September 18, 2019 14:00 - 14:25
1. Bramall - Elgar Concert Hall Aston Webb Building

14:00

#4D2 - Cloud Technologies and Case Studies - Empowering domain experts with DARE, a new cloud-based platform and working environment
DARE focuses on empowering domain experts to invent and improve their methods and models by providing a new cloud-based platform and a working environment. We have initially focused in the seismology community, supplying advance interfaces to support the Rapid Ground Motion Assessment (RA) application. It requires rapid data analyses, handling multiple data formats, multiple data sources, and availability of computing and storage resources on demand.
The new interfaces that we are building on DARE provide a fluent path from prototyping to production. Applications are not locked to platforms but can be moved to suitable new platforms without human intervention and with the encoded method’s semantics unchanged. For doing so, we exploit different technologies, such as scientific workflows (CWL), stream-based data-flow systems (dispel4py), containers (Docker), infrastructure orchestrations (Kubernetes), notebooks (Jupyter), and Cloud platforms. DARE platform acts as an intermediary between users’ applications and the underlaying computing resources, submitting applications and collecting (and storing) their provenance and results.

Speakers
avatar for Rosa Filgueira

Rosa Filgueira

Data Architect, Research Academic, University of Edinburgh, EPCC
I’m a Computer Scientist with background in High Performance and Data-Intensive Computing. I’ve been always in academia engaging with researchers and domain scientists from different domains, such as geosciences, biomedicine and most recently digital humanities. I’ve designed... Read More →


Wednesday September 18, 2019 14:00 - 14:25
4. Aston Webb, Room WG12 Aston Webb Building

14:00

#4B2 - Training, Teaching and Code Review - Submitty - an open source tool to automate marking
Have you ever had lots and lots of marking to do? Are these assignments or exams about programming? Do you have to run lots of submissions to see whether their code actually works? In this walkthrough we will show how to get Submitty [1] up and running, create an assignment and produce some submissions to show the students view. We will also talk about our experience using Submitty at UCL in a module with 100 students focusing particularly on what could go wrong and their solutions.

[1] https://submitty.org

Speakers
avatar for David Pérez-Suárez

David Pérez-Suárez

Senior Research Software Developer, UCL/RITS


Wednesday September 18, 2019 14:00 - 14:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building

14:30

#4A3 - Community and Collaboration - Analytics and Insights about Cultivating the Software Engineering Community at DLR
Software development increasingly became part of the daily work of many researchers in science and engineering. They are faced with software engineering challenges for which they are not trained. In 2005, the German Aerospace Center (DLR) started the ``DLR Software Engineering Initiative'' to support their researchers addressing these challenges. One of the initiative's core element is to setup and establish an active software engineering community within DLR.

Improving the activities of the DLR software engineering initiative is an on-going challenge. For this purpose, a good understanding of the software engineering community within DLR is required. We present insights about the DLR software engineering community through an analysis of the participation at the annual software engineering knowledge exchange workshops. These workshops can be considered as the annual software engineering community event and offer therefore a good starting point to analyze the community. In our analysis we focus on the return rate of the participants as well as the influence of the workshops topic, it's location, and the participants origins.

Speakers
avatar for Carina Haupt

Carina Haupt

Head of Software Engineering Group, German Aerospace Center (DLR)
My goal is to improve the quality of software development in research. This is what I work for and what I do research for. Whether in the field of software engineering, open source or knowledge management.


Wednesday September 18, 2019 14:30 - 14:55
1. Bramall - Elgar Concert Hall Aston Webb Building

14:30

#4D3 - Cloud Technologies and Case Studies - How to build and run an international open-data image repository
Image Data Resource (IDR, https://idr.openmicroscopy.org) is a public data repository containing over 100TB of life sciences imaging data from published studies in a searchable and reusable format. It is built from existing open-source tools but significant work was required to deploy and keep it running as a production service. I will talk about the journey from our first ever use of cloud services to scaling up a single- server system into the reliable public resource that exists today, including design choices, the mistakes we made, and the challenges we still face.

I will introduce some of the tools we use including Ansible, OpenStack, Docker and Kubernetes, but with a focus on the benefits of reproducible deployments rather than going into too much technical detail of particular tools. All of our infrastructure is open source and I will explain why, and provide links for people interested in finding out more.

This talk will hopefully provide an insight into how a public data services like this could be set up by your institution, including many of the considerations you may not have thought of.

Speakers
SL

Simon Li

Software and Operations Engineer, Open Microscopy Environment


Wednesday September 18, 2019 14:30 - 14:55
4. Aston Webb, Room WG12 Aston Webb Building

14:30

#4B3 - Training, Teaching and Code Review - Reviewing Code with GitHub
In the process of collaborative software development, the code review is a key component in ensuring that contributions meet agreed standards of style and quality. In an academic group where understanding of software engineering practices is still in its infancy, the code review has proved to be particularly mysterious, and this has given us the opportunity to develop guidelines and recommendations on how it should be conducted. This walkthrough is informed by our experience guiding software development, taking participants through an example project hosted on GitHub, from the creation of a simple Issue to the merging of a development branch.

Speakers
avatar for Andrew Williams

Andrew Williams

Research Software Engineer, University of Bristol


Wednesday September 18, 2019 14:30 - 14:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

14:30

#4C2 - Amazon Talk
TBC

Speakers
BB

Brendan Bouffler

HPC & Batch Service Team, Amazon


Wednesday September 18, 2019 14:30 - 15:00
5. Nuffield Building, Room G17 Nuffield Building

15:00

Refreshments
Tea, coffee and water will be provided along with a selection of mini filled doughnuts, chocolate jam and caramel.

Wednesday September 18, 2019 15:00 - 15:25
6. The Great Hall Aston Webb Building

15:30

#5A1 - Talk to be confirmed
Wednesday September 18, 2019 15:30 - 15:55
1. Bramall - Elgar Concert Hall Aston Webb Building

15:30

#5C1 - Tools and Case Studies - Autograd: A cool software trick for avoiding maths
With the ever-growing popularity of deep learning, much attention has been focused on tools to improve researcher efficiency. Backpropagation, the crucial step in training neural networks, is nothing but the chain rule with memoization. Autograd automates the computation of such gradients of a function. This enables the user to quickly explore the model space, by saving them from either having to code up exact analytical derivatives or make do with finite differences. This works whenever one can express a function using common differentiable python, numpy and scipy primitives (those with .deriv).
This talk will describe the algorithm behind automatic differentiation and illustrate key steps with examples. Brief guidance will follow on how to make use of Autograd within your own projects. We will finish by reviewing some of the more recent advances and the exciting use cases to which these methods are being applied!

Speakers
avatar for Pashmina Cameron

Pashmina Cameron

Sr RSE Lead, Microsoft Research Cambridge
Machine learning, Computer vision, NLP, Healthcare, C++, Python


Wednesday September 18, 2019 15:30 - 15:55
5. Nuffield Building, Room G17 Nuffield Building

15:30

#5D1 - HPC - Evaluating containerised genomics pipeline on HPC
Genomics pipelines are series of bioinformatics steps and tools/algorithms used to analyse genome data. A pipeline may run successfully in the environment in which it was created, but fail on other platforms due to differences in execution environment, which is where containers have an advantage. Genomic analyses are incredibly complex and often involve comparison of new data against multiple large-scale external datasets. High performance computing (HPC) helps to solve complex compute problems quickly and at scale.This session covers the evaluation of containerised genomics pipeline on HPC. A performance benchmark is created by comparing containerised pipeline against baremetal pipeline. Reproducibility is essential for the verification and advancement of scientific research. Containers can distribute an entire computing environment and hence support portability. This session is a showcase of work we have conducted at Hartree Centre using all open source technologies to solve real world problem that has a vital role i.e. genomics workflows. The purpose of this case study is to evaluate different container technologies and assess their feasibility and performance at HPC.

Speakers
avatar for Aiman Shaikh

Aiman Shaikh

RSE, STFC


Wednesday September 18, 2019 15:30 - 15:55
4. Aston Webb, Room WG12 Aston Webb Building

15:30

#5B1 - Testing - Testing the waters (and everything else) - QuESTing for a testing platform
Tests are an important part of any software project at every stage and tests should be at the forefront of every developer's mind. Standard testing suites have their advantages, however, it can be preferable to have a bespoke solution to your problem.

For the purpose of testing a quantum computer simulation software package QuEST (Quantum Exact Simulation Toolkit) a framework which could test all the QuEST features in a flexible way was required. QuEST is designed to be cross-platform, with serial, OMP, MPI, and GPU variants; the framework would also have to be able to handle these.

This talk will introduce the thought processes and choices behind the Python test suite we developed for this purpose. The test suite we developed interfaces directly with the C code to provide an intuitive test system with a simple test language to allow developers to prototype new "gates" by hand, and a facility to generate regression tests for these "gates", with the aim of making the final result the most simple and beneficial to the end-user.

All of this is integrated with a unified interface to be accessible with minimal effort for anyone from experts to end users, in order to encourage all users to test properly.

Speakers

Wednesday September 18, 2019 15:30 - 15:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

16:00

#5A2 - Teaching - Where do research software engineers come from? A new minor programme in CS at Lancaster University
As part of the Institute of Coding, the School of Computing and Communications at Lancaster University is creating a new minor programme. A year-long series of credit-bearing modules take non-Computer Science students through computational thinking, learning to program in JavaScript and Python, the history of computing, and teach skills in applied areas of data analytics, information visualisation, virtual worlds, and physical computing. The programme is capped by a 5-week group project for students to showcase their new skills with projects relevant to their fields. Interdisciplinary and group communication is at the heart of the programme, with lab space being redesigned to help people collaborate more effectively.
But once students have finished this programme, taking 1/3rd of their first year, what are they going to do with their skills? Are these students, developing experts in their disciplines but with Computer Science skills, the RSE's of the future? Can their home programmes deal with their skills? This talk will discuss the programme's design, intended to give practical, applied skills and widen participation from disciplines across the university, and explore the implications for RSE's identity in the future.

Speakers
avatar for Paul Dempster

Paul Dempster

Lecturer, Institute of Coding, Lancaster University
My primary interests are programming education and data analytics in education and gaming. As part of my Institute of Coding role, I am designing, implementing, and evaluating innovative Computer Science courses for non-CS major students which allow me to explore some of the questions... Read More →


Wednesday September 18, 2019 16:00 - 16:25
1. Bramall - Elgar Concert Hall Aston Webb Building

16:00

#5C2 - Tools and Case Studies - Air Quality & Python: Developing Online Analysis Tools
Poor surface air quality has a range of implications for human health and the economy. Analysing and interpreting the incoming data streams from air quality measurement stations is critical for tackling the problem and for developing early warning systems. I am using Python to develop a set of online analysis tools (ukatmos.org) to enable the public to quickly and easily plot air quality data in many ways, effectively freeing up information that is already publicly available but in awkward formats and often involves development of code. We anticipate these tools will also support data science classes at school, and can speed up scientific research by minimizing effort in repeating analyses.

The tools integrate numerous Python libraries (e.g. Pandas and NumPy), the Django web framework, the Plot.ly tools for creating interactive graphs, and SQL to address the large data volumes. Developing these Python tools in an adaptive and scalable way allows it to grow as more data become available, e.g. satellite observations. Adaptability also includes evolving user requirements. This talk will follow the processes I went through developing these tools and show a working example of the project so far.

Speakers
avatar for Douglas Finch

Douglas Finch

Postdoc Research Associate, University of Edinburgh


Wednesday September 18, 2019 16:00 - 16:25
5. Nuffield Building, Room G17 Nuffield Building

16:00

#5D2 - HPC - Pursuing and supporting reproducible workflows for all with Cylc
Cylc is a workflow engine, allowing anyone to run a custom schedule of inter-dependent tasks. Its general-purpose open-source nature has led to a technically diverse user base, from scientists & other RSEs to HPC analysts and operational forecasting staff, distributed across research centres worldwide. Development has been driven by the requirements of users; it has been a ongoing challenge to cater for the unique automation needs emerging from such varied contexts, for example building a system that scales both down, to transcend mere cron jobs, and up, to complex workflows of thousands of tasks. Hosting Cylc publicly on GitHub has been vital, enabling input, including code contributions, from all factions, and centralising communication between our international team working under inverse time zones. We invest much of our time providing training and support in the effective use of Cylc and notably at the Met Office our users have spun-up their own community group for effective and maintainable Cylc workflow design, adding the balancing act of directing, but not dictating, best practice. Hear us share our wisdom from the pursuit of reproducible workflows for all.

Speakers
avatar for Sadie Bartholomew

Sadie Bartholomew

Scientific Software Engineer, Met Office


Wednesday September 18, 2019 16:00 - 16:25
4. Aston Webb, Room WG12 Aston Webb Building

16:00

#5B2 - Testing - Improving Hardware Testing for the Large Pixel Detector Using Jupyter
As a second year computing apprentice at STFC, I was lucky enough to work in the Technology department for six months, aiding work for the Large Pixel Detector (LPD). This is a high-tech X-ray detector used in XFEL. Part of my time in the team was spent working with members of the group who build hardware for LPD and its supermodules which of require testing before they can be sent out for use. Beforehand, the testing of the tiles (that are part of the supermodules, of which there are sixteen) was done manually with the results stored using Snipping Tool and a SharePoint database – something best avoided for hours upon hours if you wish to stay sane. I used a Jupyter Notebook and some Python libraries to semi-automate this testing and compile the results into a useful UI output that contains all the information needed. I managed to implement creation of PDF files of the output. This talk will explain the project and how I went about developing it (from working with the end users to make something useful to them, to spending time evolving the code and some of the barriers I needed to overcome in order to make the project what it is today.

Speakers
MR

Matthew Richards

Software Engineering Degree Apprentice, STFC
I'm a degree apprentice at STFC training to be a software engineer. I'm in my second year of the apprenticeship, and have done a various of placements at various STFC departments. I currently work on supporting the STFC cloud, maintaining a tool that updates and tests OpenStack images... Read More →


Wednesday September 18, 2019 16:00 - 16:25
2. Aston Webb C Block Lecture Theatre Aston Webb Building

16:30

#5A3 - Teaching - RSE Summit @ Microsoft - Cloudy in Brussels
In March, Microsoft (MS) hosted a summit for EMEA Research Software Engineers in Brussels. This talk will give an overview of discussions a feature of which was how MS see RSEs as a focal point for the adoption of cloud computing for research in Higher Education. Often sitting at the interface between researchers and IT, RSEs have knowledge of both domains, work with both and teach.
Identifying and addressing knowledge gaps is an area of interest for Microsoft and following a wide-ranging discussion on training in digital skills, several themes developed which the talk will discuss: Data; Authentication; Funding; Managing Budgets; Deployment; Culture.
A recurring theme was also to identify deliverables to harness the enthusiasm of the summit. These included the report this talk summarises and a white paper on data in the cloud, but the key deliverable was the Research Software Reactor (RSR). The first workshop takes place at the end of May 2019. Using MS resources: BluePrint, DevOps and Learn, focussed initially on Azure, RSR aims to develop Proof of Concept open source deployment and learning materials for research driven workloads (https://github.com/research-software-reactor/guidelines). The talk will update on progress!

Speakers
avatar for Gerard Gorman

Gerard Gorman

Imperial College London
Azure Cloud; HPC; modelling and data inversion; DSL's and code generation; education in computational science and engineering.
avatar for James Grant

James Grant

Research Software Engineer, University of Bath
avatar for Brad Tipp

Brad Tipp

Director Higher Education Research, Microsoft Corp


Wednesday September 18, 2019 16:30 - 16:55
1. Bramall - Elgar Concert Hall Aston Webb Building

16:30

#5C3 - Tools and Case Studies - From Paper to Tech - an RSE Project on Patient Safety in Leicester Hospitals
As many as 1 in 10 patients are harmed while receiving hospital care in high income countries, indeed 1.8 million incidents were reported to NHS England in 2016-2017. Taking inspiration from aviation safety procedures, academics at the University of Leicester have been trying to track and monitor patient safety as both a learning tool for the medical students but also to improve the patient experience. However, the researchers’ initial implementation was based on a manual process in which both data-gathering and data-analysis were carried out by hand. In this talk I will share how I converted the paper forms into a mobile app (for data gathering) and an accompanying web app for data analysis. I will discuss the frameworks I used to do this, Ionic and Django, and the lessons I learnt along the way. I will also discuss how the academics and I worked together, how this benefited the project and ensured a successful outcome. I hope my experience can encourage and help other RSEs who may be facing a similar project in the future.

Speakers
avatar for Teri Forey

Teri Forey

Research Software Engineer, University of Leicester


Wednesday September 18, 2019 16:30 - 16:55
5. Nuffield Building, Room G17 Nuffield Building

16:30

#5D3 - HPC - HPC Project Assessment - Stepping into the Unknown
High Performance Computing is a bit of a paradox. On one side you have leading-edge technology, cutting frontiers in using huge quantities of data... and on the other a workhorse workflow powered by FORTRAN with very few people around to progress the code. Somewhere in the middle is you, being asked to tackle projects from how to take clearer images of a black hole to making sure that the Physics Department’s core research doesn’t grind to a halt. How do you navigate between the known, solid projects and the unknown? This talk will take you through the division lines between known and unknown in HPC projects, discuss the characteristics which define each, and go through a handy set of tips on how to assess projects and see if they are a match to your (or your team’s) skill sets. Along the way share what we have learned in commercial HPC, on the open source projects we run, and drop some serious public cloud knowledge.

Speakers
avatar for Cristin Merritt

Cristin Merritt

Sales & Marketing, Alces Flight Limited
I've been working in the field of change management for Tech for over 15 years with current work in cloud adoption for HPC. My focus is gathering together practical tools, tips, and tricks for those out there looking to manage change - and pair them with the open source, services... Read More →


Wednesday September 18, 2019 16:30 - 16:55
4. Aston Webb, Room WG12 Aston Webb Building

16:30

#5B3 - Testing - Visualising Uncertainty
There are many different representations of data values that are used in visualisations, but it is less common to see visual representations of uncertainty, especially in visualisations intended for non-technical audiences.

We have attempted to develop a visualisation method that relates uncertainty to visual complexity. We have constructed a scale of glyphs designed to work in 2D and 3D environments using R, Python and Blender, an open source 3D creation suite.

One motivation for this work is the representation of data from a network of IoT sensors. The sensors report a continuous stream of values, which is often summarised as the average over an hour. However, the quality of the sensors is not consistent and so it was necessary to find a simple but consistent way to represent the variance of the readings, so that users can understand the level of uncertainty associated with each sensor’s readings at a glance.

We will discuss the results from a series of trials designed to evaluate how users respond to the glyphs, including their ability to determine whether one glyph is more or less uncertain than another, as well as whether they are able to identify a specific glyph in context (i.e. when displayed on a map).

We submitted this talk because the visualisation of uncertainty is increasingly relevant in a number of fields and we feel that this talk will be suitable to RSEs from a range of background and subject areas, particularly those working on (or interested in) data visualisation.

Speakers
avatar for Mike Simpson

Mike Simpson

Research Software Engineer, Newcastle University
My background is in computer science and video game development. I worked in the games industry for a few years before returning to university to complete a PhD, which involved using tools and techniques from the games industry to produce real-time engineering simulations. My research... Read More →


Wednesday September 18, 2019 16:30 - 16:55
2. Aston Webb C Block Lecture Theatre Aston Webb Building

17:00

Society of RSE AGM
The AGM of the UK Research Software Engineer Association

Moderators
Wednesday September 18, 2019 17:00 - 18:00
1. Bramall - Elgar Concert Hall Aston Webb Building

19:00

Drinks Reception, pre formal dinner (Foyer)
A range of complimentary drinks will be offered in the Aston Webb Foyer and a bar will also be available accepting cash and cards.

Wednesday September 18, 2019 19:00 - 19:30
6. The Great Hall Aston Webb Building

19:30

20:30

Conference dinner sponsor's address
John McNamara is a Senior Inventor at IBM, currently leads the Senior Inventor community at IBM Hursley and is IBM UK's University Lead.

John's career in IBM began creating mainframe applications and moved on to international consultancy, where he led projects in industries and fields ranging from Banking, Pharma', Defence and Disease Control.

Prior to his current role, John was the Lead Technologist for the IBM Innovation Centre, where he helped IBM Partners to innovate with technologies such as Artificial Intelligence, IoT and Cloud.

Outside of IBM, John is a Visiting Research Fellow at the University of Portsmouth, and an Advanced Visiting Fellow at the University of Sheffield.

Speakers
avatar for John McNamara

John McNamara

Senior Inventor, IBM


Wednesday September 18, 2019 20:30 - 20:45
6. The Great Hall Aston Webb Building

21:45

Introducing the after-dinner speaker sponsored by Amazon Web Services
Speakers
BB

Brendan Bouffler

HPC & Batch Service Team, Amazon


Wednesday September 18, 2019 21:45 - 21:47
6. The Great Hall Aston Webb Building

21:45

After dinner speaker
Speakers
avatar for Dr Maggie Aderin-Pocock

Dr Maggie Aderin-Pocock

Maggie Aderin-Pocock MBE's passion is presenting science to a general audience and demonstrating that you don’t need a brain the size of a small planet to understand, participate in and enjoy science.  She has spent much of her career making novel, bespoke instrumentation ranging... Read More →


Wednesday September 18, 2019 21:45 - 22:15
6. The Great Hall Aston Webb Building
 
Thursday, September 19
 

08:30

Refreshments
Tea, coffee and water will be provided in the Great Hall.

In the Aston Webb Building near to the registration/reception desk, a cloakroom is available in room G30 along with a quiet room in G31.

Thursday September 19, 2019 08:30 - 09:00
6. The Great Hall Aston Webb Building

08:45

Posters available to view from 9am to 3pm
Thursday September 19, 2019 08:45 - 15:00
10. Mezzanine Floor, (First floor), Bramall Foyer Bramall Elgar Concert Hall, Above Costa coffee

09:00

#6W1a - IBM PowerAI : An introduction and overview
Register here if you plan to attend this session: http://ibm.biz/RSEConf19

With Deep Learning and AI becoming much more common in the world of research, a new set of skills need to be developed. These skill will include more extensive use of Python and management of various libraries and plug ins, as well as knowledge of common Machine Learning and Deep Learning frameworks. Software like Tensorflow, PyTorch, and Caffe are becoming more prevalent, with interaction via Python and Jupyter notebooks.

This session is an introduction to the hardware and software products available from IBM Systems to support the development and deployment of your Machine Learning and Deep Learning workloads. We will focus on the capabilities and tools available, as well as the common use cases, and how best to deploy and utilise these tools for Research. This will include: The AC922 server, based on the POWER9 processor with NVLink for high bandwidth, Low latency connection to NVIDIA Tesla V100 GPUs. No charge software bundle incorporating optimised versions of the common Deep Learning frameworks (Tensorflow, PyTorch, Caffe). Enterprise AI development tools including Watson Machine Learning Accelerator, Watson Studio, and H2O Driverless AI. PowerAI Vision training and inference offerings for rapid development of Deep Learning imaging jobs. Deployment methodologies - whole system, containerised, multi-tenancy, scheduler based. Unique capabilities of the IBM platform, such as Large Model Support and SnapML for accelerated Machine Learning.

Speakers
avatar for Tom Farrand

Tom Farrand

Machine Learning Engineer, IBM
avatar for Andrew Laidlaw

Andrew Laidlaw

AI Infrastructure Specialist, IBM


Thursday September 19, 2019 09:00 - 10:30
2. Aston Webb C Block Lecture Theatre Aston Webb Building

09:00

#6W2a - GUIs for Python - improving the accessibility of scientific software (part 1)
Research software has been a driving force behind the birth and rapid growth of informatics, but it was the appearance of graphic user interfaces (GUI) in the 1980s that made computers accessible to everyone. A GUI helps to reduce the learning curve for using software, increases the base of potential users and can ultimately increase citations and impact. Moreover, a well-designed GUI can perform validation and increase the robustness and reproducibility of the results, productively decoupling developers from users.

This workshop will have three parts. In the first one, we will give an introduction to GUIs and review three of the most common Python packages to create them: Tkinter for the desktop, Jupyter Widgets for web and Kivy for mobile devices (45 min). The second part will be a hands-on session where attendees will go through a range of exercises to code a complete GUI using the package of their choice (90 min). The last part will provide guidance on how to plan and implement a GUI, considering users’ objectives, accessibility, gathering feedback, providing contextual help, etc. At the end of the workshop attendees will have time to come up with an actionable plan to apply these to their own research software (45 min).

Speakers
avatar for Diego Alonso Álvarez

Diego Alonso Álvarez

Research Software Engineer, Imperial College London


Thursday September 19, 2019 09:00 - 10:30
3. Dome Lecture Theatre (access via stairs only) Aston Webb Building

09:00

#6W3a - Build a BinderHub for hosting Reproducible Software in the Cloud (part 1)
PREREQUISITES:
To participate in this workshop, you will need a Microsoft Azure account. Sign up for a free trial here: https://azure.microsoft.com/en-gb/free/
You will asked to provide a credit card for identity purposes only - you will NOT be charged. Please also do NOT use an .ac.uk domain email address to sign up as this might cause problems during deployment.

You will also need a Docker Hub account, please sign up here: https://hub.docker.com/signup

Familiarity with the command line is also useful.

DESCRIPTION:
BinderHub is a Cloud-based, multi-user server technology that captures the computing environment of a Git repository within a Docker image. It then provides an interactive browser from which code can be run in the environment under which it was developed without placing installation responsibilities on the user. A unique URL to this browser is generated making the software easily sharable with collaborators. BinderHubs can be built anywhere in the world and are Cloud-neutral. Building an in-house BinderHub is advantageous as it would facilitate the use of private repositories and make available a greater variety of computing resources - facilities which are not currently available on the public Binder service.

By harnessing the power of Cloud computing and building a BinderHub with expanded capabilities, scientific analyses can become more accessible and transparent to the wider community. BinderHubs can showcase the reproducibility of software as well as being a valuable teaching or demonstration tool.

In this workshop, attendees will learn how to deploy a BinderHub on Microsoft Azure and connect with others who have or are interested in doing so.

Speakers
avatar for Sarah Gibson

Sarah Gibson

Research Data Scientist, The Alan Turing Institute
Among other projects, I was a core team member behind The Turing Way (https://the-turing-way.netlify.com/introduction/introduction, https://github.com/alan-turing-institute/the-turing-way) which produced a handbook to reproducible data science. I am also a mybinder team member. I'm... Read More →


Thursday September 19, 2019 09:00 - 10:30
5. Nuffield Building, Room G17 Nuffield Building

09:00

#6W4a - Better Code, Faster with Kubernetes in Google Cloud (part 1)
Learn how Google Cloud Platform can help you build secure and resilient applications that can scale to the needs of your research. During this workshop you'll get hands-on and learn Kubernetes fundamentals live with a Google Cloud trainer. The hands-on lab will show you how to deploy a containerized application with Kubernetes Engine.

Speakers
avatar for Andres-Leonardo Martinez-Ortiz

Andres-Leonardo Martinez-Ortiz

Google
Andres-Leonardo Martinez-Ortiz a.k.a almo is a member of the Google Engineering team, leading Google Cloud Ecosystem program in Europe. Based in Zurich, he drives the success of Google's developer products and the Open Web by creating a thriving ecosystem of developers. He meets with... Read More →


Thursday September 19, 2019 09:00 - 10:30
4. Aston Webb, Room WG12 Aston Webb Building

10:30

Refreshments
Tea, coffee, water and biscuits will be provided in the Great Hall.

Thursday September 19, 2019 10:30 - 10:55
6. The Great Hall Aston Webb Building

11:00

#6W1b - Train the Trainer: IBM PowerAI - Hands On with Accelerated Software and Hardware For AI Workloads
Register here if you plan to attend this session as there is limited availability: http://ibm.biz/RSEConf19

A Laptop is required for this workshop

An in depth hands on session covering some of the major benefits of using GPU accelerated systems for building Deep Learning (DL) and Machine Learning (ML) models. This is based on the IBM Watson Machine Learning Community Edition software bundle, free for use on IBM Power Systems (AC922) and x86 based GPU accelerated systems. In addition to setting up environments to allow data scientists access to Deep Learning frameworks, we will also show you how to use features like:

Large Model Support (LMS) Available for Tensorflow and PyTorch, LMS allows for more complex models and larger data points than can generally fit into GPU memory. Out of memory errors are common for data scientists, and can be alleviated by LMS by using system memory alongside GPU memory space. We will show you 3 techniques for implementing LMS with existing code and with minimal effort.

SnapML Common ML algorithms can be accelerated by using GPU parallelism and the right approach. We will show how to use the GPU accelerated algorithms in SnapML to offload common functions to accelerated hardware, providing performance boosts of up to 50x. This can be used in place of the extensively used SciKit Learn Python library to simplify the implementation.

Distributed Deep Learning (DDL) Scaling beyond a single GPU or a single server can be a challenge for data science workloads, particularly for Deep Learning. DDL allows users to scale their existing model training runs across any available resources - maximising efficiency and leading to faster results. With up to 95% linear scalability across 256 GPUs, we will demonstrate how to make use of this scalability for existing code.

PowerAI Vision When you come across users who do not have the Python skills or Deep Learning knowledge to build their own models based on visual data, then other tools are available. PowerAI Vision can be used exclusively through the web interface to build and label data sets, train deep learning models, and even deploy them as public APIs. This software allows researchers with image data stores to rapidly build models for:
  • Image classification
  • Object detection
  • Object segmentation
  • Action recognition

Speakers
avatar for Tom Farrand

Tom Farrand

Machine Learning Engineer, IBM
avatar for Andrew Laidlaw

Andrew Laidlaw

AI Infrastructure Specialist, IBM


Thursday September 19, 2019 11:00 - 12:30
2. Aston Webb C Block Lecture Theatre Aston Webb Building

11:00

#6W2b - GUIs for Python - improving the accessibility of scientific software (part 2)
Part 2 of this workshop.

Speakers
avatar for Diego Alonso Álvarez

Diego Alonso Álvarez

Research Software Engineer, Imperial College London


Thursday September 19, 2019 11:00 - 12:30
3. Dome Lecture Theatre (access via stairs only) Aston Webb Building

11:00

#6W3b - Build a BinderHub for hosting Reproducible Software in the Cloud (part 2)
Part 2 of this workshop. You will have to have attended Part 1 in order to participate in Part 2.

PREREQUISITES:
To participate in this workshop, you will need a Microsoft Azure account. Sign up for a free trial here: https://azure.microsoft.com/en-gb/free/
You will asked to provide a credit card for identity purposes only - you will NOT be charged. Please also do NOT use an .ac.uk domain email address to sign up as this might cause problems during deployment.

You will also need a Docker Hub account, please sign up here: https://hub.docker.com/signup

Familiarity with the command line is also useful.

DESCRIPTION:
BinderHub is a Cloud-based, multi-user server technology that captures the computing environment of a Git repository within a Docker image. It then provides an interactive browser from which code can be run in the environment under which it was developed without placing installation responsibilities on the user. A unique URL to this browser is generated making the software easily sharable with collaborators. BinderHubs can be built anywhere in the world and are Cloud-neutral. Building an in-house BinderHub is advantageous as it would facilitate the use of private repositories and make available a greater variety of computing resources - facilities which are not currently available on the public Binder service.

By harnessing the power of Cloud computing and building a BinderHub with expanded capabilities, scientific analyses can become more accessible and transparent to the wider community. BinderHubs can showcase the reproducibility of software as well as being a valuable teaching or demonstration tool.

In this workshop, attendees will learn how to deploy a BinderHub on Microsoft Azure and connect with others who have or are interested in doing so.

Speakers
avatar for Sarah Gibson

Sarah Gibson

Research Data Scientist, The Alan Turing Institute
Among other projects, I was a core team member behind The Turing Way (https://the-turing-way.netlify.com/introduction/introduction, https://github.com/alan-turing-institute/the-turing-way) which produced a handbook to reproducible data science. I am also a mybinder team member. I'm... Read More →


Thursday September 19, 2019 11:00 - 12:30
5. Nuffield Building, Room G17 Nuffield Building

11:00

#6W4b - Better Code, Faster with Kubernetes in Google Cloud (part 2)
This is the second half of this workshop: https://sched.co/QT69

Speakers
avatar for Andres-Leonardo Martinez-Ortiz

Andres-Leonardo Martinez-Ortiz

Google
Andres-Leonardo Martinez-Ortiz a.k.a almo is a member of the Google Engineering team, leading Google Cloud Ecosystem program in Europe. Based in Zurich, he drives the success of Google's developer products and the Open Web by creating a thriving ecosystem of developers. He meets with... Read More →


Thursday September 19, 2019 11:00 - 12:30
4. Aston Webb, Room WG12 Aston Webb Building

12:30

Lunch and notices
A cold fork buffet will be provided in the Great Hall.


Thursday September 19, 2019 12:30 - 13:25
6. The Great Hall Aston Webb Building

13:30

#6W5a - Building a team culture that ensures sustainability, passion, and productivity (part 1)
In this interactive workshop we explore how meeting technical objectives depends critically on meeting cultural challenges within teams. Many small teams evolve naturally on a positive path because teams are often formed by friendly collaborators with common interests and goals. But as teams grow they face new challenges, including fragmented time commitments, physically distributed developers, and growing numbers of stakeholders. These challenges make it significantly harder to maintain a healthy team culture. Although agile methodologies and modern software tools can help developers manage these challenges, these processes alone are insufficient. Thus, a growing number of teams are combining these methodologies with techniques that support a passionate and collaborative culture. We explore lightweight progress tracking, informal "tea-time", virtual scrums, human-centered design, empathy building, listening games and exercises. The session is 120 min of guided small group exercises and debriefing, followed by 30 min of large group discussion and 30 min retrospective. We recap lessons learned and explore how culture affects team performance. We focus on skills building in interpersonal communication and inclusion.

Speakers
avatar for Elaine M. Raybourn

Elaine M. Raybourn

Principal Member of the Technical Staff, Applied Cognitive Science, Sandia National Laboratories


Thursday September 19, 2019 13:30 - 15:00
2. Aston Webb C Block Lecture Theatre Aston Webb Building

13:30

#6W6a - Oracle Workshop (part 1)
1.30 – 2.30 Session 1: “Creating scalable, heterogeneous Clusters in the Cloud” 
Presented by: Dr Matt Williams & Dr. Christopher Woods - University of Bristol
Abstract: Learn how you can launch a scalable, heterogeneous Cluster in the Cloud in Oracle's cloud which only charges you for what you use. This workshop will walk you through the steps from getting your cloud account up to running jobs on a familiar batch environment. Discover how to monitor the status of the cluster and how to shut the whole thing down at the end.

2.30 – 3.00 Session 2 (part 1): “Fast Queries with Huge Datasets - using SQL, Graphs and advanced database techniques to crunch large data sets” 
Presented by: Rich Pitts & Mike Riley

3.00 – 3.30 Refreshments

3.30 – 4.00 Session 2 (part 2): “Fast Queries with Huge Datasets - using SQL, Graphs and advanced database techniques to crunch large data sets” 
Presented by: Rich Pitts & Mike Riley

4.00 – 5.00 Session 3: “Kubnernetes and Fn Project - creating large distributed workloads without owning a HPC cluster” 
Presented by: Thom Leggett
Abstract: Serverless technology such as Functions-as-a-Service platforms enable research teams to focus on solving their domain problems without having to be an IT infrastructure expert. Their unique pay-as-you-go model allows you to then run these workloads at large scale without having to maintain a cluster of your own. In this workshop we will build and run a large distributed workload using the Fn Project and Oracle Functions. We will discuss when using a serverless platform is appropriate and when you might need something with more capabilities. We will then take a look at how Kuberenetes can help you meet those more demanding needs.

This agenda covers both this workshop session and the following Oracle Workshop  (part 2).

Speakers
avatar for Christopher Woods

Christopher Woods

Research Software Engineer, University of Bristol
I'm the Head of the Research Software Engineering Group (HoRSE) at the University of Bristol and am one of the first cohort of EPSRC RSE Fellows. I've been involved with the RSE community for many years now, and am Talks Chair for RSE19. Obviously I'm biased, but I think this will... Read More →
avatar for Matt Williams

Matt Williams

Research Software Engineer, University of Bristol
Matt works at the University of Bristol in the JGI as a Research Software Engineer. Matt joined the University in 2016, coming from the University of Birmingham where he provided support for the LHC's world-wide computing platform. He worked to support the synthetic biology community... Read More →
avatar for Thom Leggett

Thom Leggett

Engineering Director, Oracle
Thom works on serverless computing at Oracle, specifically the open source Fn Project. He and team design, develop, test and operate Oracle's Functions-as-a-Service (FaaS) platform. He has spent his career to date delivering on global-scale consumer-facing apps and infrastructure-as-a-service... Read More →
avatar for Mike Riley

Mike Riley

Mike Riley works as a Solution Engineer within the Oracle technology Presales team in the UK.He has worked for Oracle for over 20 years within Technical Roles focusing primarily on the database. He graduated from North Staffordshire Polytechnic (when it was still a Polytechnic) with... Read More →
avatar for Rich Pitts

Rich Pitts

Rich Pitts is a Solution Architect within the Oracle technology Presales team in the UK Initial career was a Research Scientist at York University, then engaged on projects in Belize, Saudi Arabia, and Kenya. He then moved into main stream IT with real time and database systems. He... Read More →


Thursday September 19, 2019 13:30 - 15:00
3. Dome Lecture Theatre (access via stairs only) Aston Webb Building

13:30

#6W7a - Be an RSE Superhero with VS Code and Azure Pipelines (part 1)
In this workshop, we will show you how you can incorporate VS Code and Azure Pipelines into your day-to-day workflow as an RSE, helping you to be more productive and accomplish common tasks with greater ease.

VS Code is an easily extensible, cross-platform code editor that has support for a wide array of different languages and toolchains. We will show you how extensions like Live Share (which let small groups edit the same files in different editors), Azure Tools (which provides a rich suite of interactions with Azure) and Remote Development (which lets you work locally but run code remotely) can give you RSE superpowers in your day-to-day work. We will also walk you through how to use Azure Pipelines to provide simple yet powerful Continuous Integration and Deployment functionality for your projects, from multi environment testing to automated building and deployment of your solutions. Come along and learn how VS Code and Azure Pipelines can empower you to do more.

Speakers
avatar for Matthew Johnson

Matthew Johnson

RSE, Microsoft
avatar for Tania Allard

Tania Allard

RSE conference diversity and accessibility chair, Microsoft


Thursday September 19, 2019 13:30 - 15:00
5. Nuffield Building, Room G17 Nuffield Building

13:30

#6W8a - Getting the most out of the modern C++ language and standard libraries
We all want to write efficient and expressive code that is free from bugs, quick to write, and easy to read. That’s not always been possible, but as the C++ language and libraries evolve it’s becoming the language to choose to achieve these goals. But with so many changes since 2011 it’s a daunting task to keep up-to-date with the features and best practices that will save you time at every stage of your workflow. In this hands-on workshop we will start with a pre-prepared ‘old’ piece of code and collaboratively utilise new language and library features to rewrite it. We will make use of the algorithms library, smart pointers, lambda functions, the filesystem library and much more, with features spanning modern C++ standards up to and including C++20. The resulting ‘new’ code will be more concise, less error-prone, easier-to-maintain and conform to the C++ Core Guidelines. This workshop will not only familiarise you with language and library features that you may be unaware of, but also help you to recognise patterns of code that could be (re)written with algorithms or new library functionality. This will be a fun, live-coding experience that will leave you better prepared to fully leverage the latest and greatest of modern C++.

Speakers
avatar for Graham Lee

Graham Lee

Head Labrarian, Labrary Ltd.
I make it easier and faster to make high-quality software that respects people's privacy and freedom. You can find me in universities or in companies, but that's probably what I'll be doing. Talk to me about continuous delivery, devops, team performance, measuring success, Python... Read More →
avatar for Fergus Cooper

Fergus Cooper

Research Software Engineer, University of Oxford
I am currently working as a research software engineer at the University of Oxford, having helped found the Oxford RSE group in December 2018. Since then, the group has more than doubled in size, and we’re looking forward to collaborating with the UK RSE community and with the open... Read More →
MR

Martin Robinson

Research Software Engineer, University of Oxford


Thursday September 19, 2019 13:30 - 15:00
4. Aston Webb, Room WG12 Aston Webb Building

15:00

Refreshments
Tea, Coffee, water and a selection of mini cakes... apple & cinnamon sponge, chocolate fondant, forest fruit cheesecake, custard crumble sponge & coconute sponge.

Thursday September 19, 2019 15:00 - 15:25
6. The Great Hall Aston Webb Building

15:30

#6W5b - Building a team culture that ensures sustainability, passion, and productivity (part 2)
Part 2 of this workshop.

Speakers
avatar for Elaine M. Raybourn

Elaine M. Raybourn

Principal Member of the Technical Staff, Applied Cognitive Science, Sandia National Laboratories


Thursday September 19, 2019 15:30 - 17:00
2. Aston Webb C Block Lecture Theatre Aston Webb Building

15:30

#6W6b - Oracle Workshop (part 2)
This is the continuation of Oracle Workshop (part 1). For the agenda please see Oracle Workshop (part 1).

Speakers
avatar for Christopher Woods

Christopher Woods

Research Software Engineer, University of Bristol
I'm the Head of the Research Software Engineering Group (HoRSE) at the University of Bristol and am one of the first cohort of EPSRC RSE Fellows. I've been involved with the RSE community for many years now, and am Talks Chair for RSE19. Obviously I'm biased, but I think this will... Read More →
avatar for Matt Williams

Matt Williams

Research Software Engineer, University of Bristol
Matt works at the University of Bristol in the JGI as a Research Software Engineer. Matt joined the University in 2016, coming from the University of Birmingham where he provided support for the LHC's world-wide computing platform. He worked to support the synthetic biology community... Read More →
avatar for Thom Leggett

Thom Leggett

Engineering Director, Oracle
Thom works on serverless computing at Oracle, specifically the open source Fn Project. He and team design, develop, test and operate Oracle's Functions-as-a-Service (FaaS) platform. He has spent his career to date delivering on global-scale consumer-facing apps and infrastructure-as-a-service... Read More →
avatar for Mike Riley

Mike Riley

Mike Riley works as a Solution Engineer within the Oracle technology Presales team in the UK.He has worked for Oracle for over 20 years within Technical Roles focusing primarily on the database. He graduated from North Staffordshire Polytechnic (when it was still a Polytechnic) with... Read More →
avatar for Rich Pitts

Rich Pitts

Rich Pitts is a Solution Architect within the Oracle technology Presales team in the UK Initial career was a Research Scientist at York University, then engaged on projects in Belize, Saudi Arabia, and Kenya. He then moved into main stream IT with real time and database systems. He... Read More →


Thursday September 19, 2019 15:30 - 17:00
3. Dome Lecture Theatre (access via stairs only) Aston Webb Building

15:30

#6W7b - Be an RSE Superhero with VS Code and Azure Pipelines (part 2)
This is the second part of https://sched.co/QT6a

Speakers
avatar for Matthew Johnson

Matthew Johnson

RSE, Microsoft
avatar for Tania Allard

Tania Allard

RSE conference diversity and accessibility chair, Microsoft


Thursday September 19, 2019 15:30 - 17:00
5. Nuffield Building, Room G17 Nuffield Building

15:30

#6W8b - Using Arm HPC Systems and Software Ecosystem
Here in the UK, we have Isambard (Cray XC50) and three Catalyst (HPE Apollo 70) Arm HPC systems.

This workshop will give you a chance to use an Arm HPC system to test your code, ask questions about the Arm HPC Ecosystem, and find out how easy it is to use such a system.

Please bring along your own code, or try out some examples. 

Find out more about the Arm HPC Ecosystem https://developer.arm.com/solutions/hpc 

and how to build several software packages at 

https://gitlab.com/arm-hpc/packages/wikis/categories/allPackages



Speakers
PR

Phil Ridley

Staff Field Applications Engineer, Arm


Thursday September 19, 2019 15:30 - 17:00
4. Aston Webb, Room WG12 Aston Webb Building