Research Software Engineering

EDI Talk: Why Do We Need Diversity in Research Software Engineering

On Thursday 22nd May the EDI committee hosted a talk on “Why Do We Need Diversity in Research Software Engineering?” by the Software Sustainability Institute Fellows Deborah Udoh (OLS) https://www.software.ac.uk/fellowship-programme/deborah-udoh and Olexandr Konovalov (St Andrews) https://www.software.ac.uk/fellowship-programme/olexandr-konovalov. On display we had a collection of posters designed by students to promote and raise awareness of EDI aspects, and celebrate cultural differences in the School and in our discipline. This was accompanied by coffee and cakes.

This talk was the story of two members of the global research software community whose paths converged thanks to the Software Sustainability Institute. One a Ukrainian mathematician and computer scientist in Scotland, the other a Nigerian nurse in tech – they are from vastly different backgrounds, but share more in common than meets the eye, and have already begun to shape an inclusive future for researchers from all walks of life.

Through lived experiences, they explored the real-world barriers they faced – from underrepresentation and visa limitations to the invisible weight of imposter syndrome — and the communities and infrastructures that helped them keep going: OLS, the Carpentries, and the SSI.

They spoke of using their platforms to build better pathways into research and research software engineering, especially for those who never imagined they belonged in these spaces, and how institutions, allies, and community members play an active role in creating more equitable, mentally healthy spaces — and why your involvement matters.

Research Software Group Lunchtime Seminar – Friday 23rd May

There will be a Research Software Group Lunchtime Seminar on Friday May 23rd at 1pm, in room 1.33B.

Talk Title: “People First: Sustaining Research Software by Sustaining the People Who Build It”

Speakers are Software Sustainability Institute Fellows: Deborah Udoh (OLS) and Olexandr Konovalov (St Andrews)

– https://www.software.ac.uk/fellowship-programme/deborah-udoh

– https://www.software.ac.uk/fellowship-programme/olexandr-konovalov

Abstract

What does it mean to build sustainable research software—and sustainable research software communities?

Too often, sustainability is framed in terms of clean code, reproducibility, funding and long-term maintenance. But sustainability is also about people: who gets to stay, who gets to lead, and who burns out or leaves before their potential is fully realised.

This talk invites us to look beyond technical best practices and consider the human infrastructure that truly sustains research software: the developers, contributors, maintainers, and collaborators who often work in the margins of recognition. We’ll explore how issues like burnout, impostor syndrome, and lack of psychological safety threaten not just individual wellbeing, but the continuity and health of the software ecosystems we care about.

Using real-world examples from both academic and open-source contexts, we’ll share practices and small culture shifts that have helped sustain people in research software roles.

This session will include a short, interactive exercise where participants will reflect on their own sustainability needs, and collectively brainstorm people-first practices for healthier RSE communities.

Open source contributors sought for an interview

MANAGING OPEN SOURCE PROJECTS ON GITHUB — SUCCESS FACTORS AND PERFORMANCE INDICATORS

As a part of my, Julia Seeger’s, MSc Dissertation in the School of Computer Science at the University of St Andrews I am looking for volunteers for an interview. This interview is a part of a research project focussed on success factors and performance indicators of managing open source projects hosted on GitHub.

I am looking for core contributors to open source projects hosted on GitHub. Ideally, the project should have configured and make use of Travis CI, and should have a history of pull requests before and after the configuration of Travis CI.

I would firstly be interested in your opinion about success factors and performance indicators that I have identified by analysing the public GitHub repository of your project with the help of the GitHub API. I will ask if, as a core contributor of the project, you would agree or disagree with my findings. Secondly, I am interested in your personal experience in managing a repository of an open source project on GitHub, and the factors and managing techniques you identified to be important for a successful project.

The interview will take place in a form of a video or an audio call via Skype for Business or Microsoft Teams. The interview will take place during July 2020, consists of 6 questions and will last around 25 minutes. If you agree to participate, questions will be given to you at least three days in advance.

If you are willing to participate, please get in touch using the contact details below. You will then be given a Participant Information Sheet that further details my research, and will have the opportunity to ask questions, before being asked whether you consent to participate.

Contact Details

Researcher: Julia Seeger
js433@st-andrews.ac.uk

Supervisor: Dr. Olexandr Konovalov
obk1@st-andrews.ac.uk

Modern practices of sharing computational research

As a part of the Love Data Week, Olexandr Konovalov will give a talk on Tuesday 11 February, 3pm, Physics Lecture Theatre C.

Abstract: Have you been frustrated by trying to use someone else’s code which is non-trivial to install? Have you tried to make supplementary code for your paper to be easily accessible for the reader? If so, you certainly know that this may require non-trivial efforts. I will demonstrate some tools that may help to create reproducible computational experiments, and will explain which skills will be needed to use these tools. The talk will demonstrate examples in Python and R runnable in Jupyter notebooks. You are welcome to bring your laptop to try these examples online. No prior knowledge of programming is required.

Links:

  • Templates for reproducible experiments in GAP, Python and R
  • Code4REF guidance on recording research software in Pure

References:

Event details

  • When: 11th February 2020 15:00 - 16:00
  • Where: Phys Theatre C
  • Format: Talk

Georgios Gerasimou (University of St Andrews): Frontiers in computational revealed preference analysis

RESCHEDULED: please note the changed date and a non-standard time!

Abstract: Prest is a recently published piece of open-source software for computational revealed preference analysis that provides novel ways to estimate decision makers’ preferences over choice alternatives by analysing their observable choice behaviour. This software is informed by classic as well as recent developments in economic revealed preference theory. Some of the recent developments take the form of models that are computationally complex. This complexity currently hinders the inclusion of these models in the Prest toolkit. The presentation will first aim to describe the primary ideas underpinning Prest and illustrate them with examples from its existing toolkit. It will then proceed with a discussion of some of the challenges pertaining to the expansion of that toolkit with more models and operations. The presentation will be self-contained and no prior background in economics will be necessary.

Speaker Bio: Georgios is a Reader in Economics at the University of St Andrews, working mainly on decision theory and revealed preference analysis. In the latter research programme, Georgios’ work aims to improve our understanding of people’s decision processes and preferences through theoretical, experimental/empirical as well as computational methods. Georgios co-developed the Prest software program for computational revealed preference analysis (https://prestsoftware.com/).

Event details

  • When: 17th February 2020 14:00 - 15:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar

Need new software or an interface? Our students can help you design it for free! First deadline Friday 20th December

We are looking for five projects from within the University that have to do with creating new software and/or hardware. Suitable projects can come from individual researchers, practitioners/companies, Schools, or any Departmental Unit that is thinking about building some software or hardware system that will be facing humans (this includes the public, but also experts of any kind or any type of populations, such as children).

The MSc students of our module CS5042 – User Centered Interaction Design – will be performing a contextual analysis of the environment, extracting user interface requirements and providing up to a medium level fidelity design prototype, with the option to further taking this on to working prototype stage during their MSc project during the summer.

In the past, our students have successfully completed designs for the following types of systems:

  • Interactive exhibitions for museums and Edinburgh City of Culture
  • A health smartphone application interface for CIGNA, a health insurance provider
  • An integrated public display messaging system for the library
  • An interactive entrance welcoming system for the entrance of the School of Computer Science
  • An interactive laterality testing tool for the School of Medicine
  • An interface design for a system which measures peoples vital signals at a distance using cameras for Beyond Medics Limited
  • Novel web-based and mobile applications to explore literary collections

If you think your project could use this kind of help, please send to us by e-mail (cs5042.lec@cs.st-andrews.ac.uk):

  • Your name, e-mail address, and phone number
    A sentence or two about what kind of project you have in mind

We will then get in contact with you to briefly explore the options. No commitment necessary at this point. Everything is, of course, free, and this could be a great opportunity for you to explore a tentative system, even if you are not sure that you will need it.

Thank you very much for considering this.

Please feel free to forward this far and wide to other colleagues who may find this useful.

Many thanks,

Uta Hinrichs and Kenneth Boyd

cs5042.lec@cs.st-andrews.ac.uk

IBANS drop-in session

IBANS (Institute of Behavioural and Neural Sciences) will be running the first drop-in session of on December 11th at 3pm in the Seminar Room in the Psychology & Neuroscience building (first floor). Niki Khan (School of Psychology and Neuroscience) writes:

“The drop-in sessions are designed to be periodic social events with catering, where people can meet each other, get help with their experiments, discuss prospective collaborations, knowledge exchange etc. We are envisaging questions on study design, programming (Python, R, other), version control, visualisations, and other topics. At the first of such meetings (on Dec 11th), we will discuss with those who will come what we would like to do next. These sessions may be especially useful for those who have attended  Software Carpentry training, and now would like to further practice and master their computational skills.“

Event details

  • When: 11th December 2019 15:00

Daniel S. Katz (University of Illinois): Parsl: Pervasive Parallel Programming in Python

Please note non-standard date and time for this talk

Abstract: High-level programming languages such as Python are increasingly used to provide intuitive interfaces to libraries written in lower-level languages and for assembling applications from various components. This migration towards orchestration rather than implementation, coupled with the growing need for parallel computing (e.g., due to big data and the end of Moore’s law), necessitates rethinking how parallelism is expressed in programs.

Here, we present Parsl, a parallel scripting library that augments Python with simple, scalable, and flexible constructs for encoding parallelism. These constructs allow Parsl to construct a dynamic dependency graph of components from a Python program enhanced with a small number of decorators that define the components to be executed asynchronously and in parallel, and then execute it efficiently on one or many processors. Parsl is designed for scalability, with an extensible set of executors tailored to different use cases, such as low-latency, high-throughput, or extreme-scale execution. We show, via experiments on the Blue Waters supercomputer, that Parsl executors can allow Python scripts to execute components with as little as 5 ms of overhead, scale to more than 250000 workers across more than 8000 nodes, and process upward of 1200 tasks per second.

Other Parsl features simplify the construction and execution of composite programs by supporting elastic provisioning and scaling of infrastructure, fault-tolerant execution, and integrated wide-area data management. We show that these capabilities satisfy the needs of many-task, interactive, online, and machine learning applications in fields such as biology, cosmology, and materials science.

Slides: see here.

Speaker Bio: Daniel S. Katz is Assistant Director for Scientific Software and Applications at the National Center for Supercomputing Applications (NCSA), and Research Associate Professor in Computer Science; Electrical & Computer Engineering; and the School of Information Sciences at the University of Illinois Urbana-Champaign. For further details, please see his website here.

Event details

  • When: 18th October 2019 13:00 - 14:00
  • Where: Cole 1.33b
  • Series: School Seminar Series
  • Format: Seminar

Code4REF: Recording software outputs in Pure

Do you develop research software?  If so, you may be interested in the Code4REF project, which explains how to record it in Pure – the research information system used in St Andrews. Research software is a primary research output, and it should get the same visibility as research publications on the University research portal. You can find all current software entries in the Research Portal here, but the picture is certainly incomplete – we know many more researchers who write code. We call everyone to join efforts and help us to collect further evidence that software is vital for research!

If you have any comments about the Code4REF project, please create an issue in its GitHub repository.

Software Carpentry Workshop

Registration is open for the next Software Carpentry workshop in St Andrews on September 23-24 in the Parliament Hall. We will teach UNIX shell, version control with Git and programming with Python. Please see the workshop page for further details and the link to registration via PDMS.

Event details

  • When: 23rd September 2019 - 24th September 2019
  • Where: Parliament Hall
  • Format: Workshop