Blog posts

Highlights from RSECon22 from the central RSE team

By the whole RSE Team

Overview

This year, the annual conference organised by the Society of Research Software Engineering was back on as an in-person event for the first time since 2019. This meant that for many of the college’s central RSE team it was their first opportunity to meet up with RSEs from across the country and further afield. The College was well represented, with five delegates attending from the central team along with RSEs based in specific departments, research groups and teaching staff from the Graduate School.

Overall, the conference was an excellent opportunity to strengthen old connections and make new ones, with plenty of opportunities for networking. The mix of talks, posters, panel discussions, tutorials and walkthroughs covered a wide range of topics from the highly technical to more community-focused issues. Although it is impossible to cover the whole event in detail, we have summarised some of our personal highlights below. The full set of recorded presentations should be available on the SocRSE Youtube channel soon.

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Fine Tuning Django User Permissions

Fine Tuning Django User Permissions

Dr Dan Davies from the Imperial RSE team has written a how-to guide based on his experiences with the Django web framework for python. Read the full blog post here.

The RSE team is involved in an increasing number of software projects requiring a front-end web app. The main advantage to having a web app element for your research software is that users can interact with it via a web browser, without having to install anything to their local machine. There are of course downsides, including the need to deploy, host and maintain software somewhere suitable. However, there is a wide range of popular frameworks to make the whole process a lot smoother.

User permissions are an important consideration for any web app. This is not necessarily just to do with overall security, but how you might want different types of users – with different roles – to interact with your software. For example, it is common to require admin users to be able to perform a wide variety of actions, while the majority of users should only be able to perform a small subset of actions. The degree of complexity required will depend on the overall aim.

We frequently use the Django web framework, which facilitates the creation of web apps solely in Python. This blog post covers aspects of user management and permissions within Django, which Dan has learned about and implemented while working on a web-based database to store and visualise sets of experimental data. It covers some basics such as how to assign permissions to user and groups of users, as well as more advanced topics such as setting up automatic permissions when specific objects are created. We hope it will be useful to the wider RSE community and beyond!

Simple permission assignment in Django
Fig. 1: Simple permission assignment in Django
Automatic permission assignment for specific objects in Django.
Fig. 2: Automatic permission assignment for specific objects in Django.

Building Research Software Communities

Building Research Software Communities: Running a workshop on community building and sustainability for the research software community

Michelle Barker, Jeremy Cohen, Daniel Nüst, Toby Hodges, Serah Njambi Rono, Lou Woodley

On Wednesday 17th March 2021, around 50 individuals from a wide range of different countries and time zones came together for the first of two 2-hour sessions that formed our “Building Research Software Communities: How to increase engagement in your community” workshop.

Run as part of the SORSE Series of Online Research Software Events, this workshop brought together an organising team consisting of 3 members of the international research software community and a group of speakers including experts in community engagement and sustainability. In this blog post we provide an overview of the workshop and some of the key messages and outcomes.

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Research Software Directories

This is a summary of a SORSE discussion session, presented by:

  • Mark Woodbridge, Imperial College London
  • Vanessa Sochat, Stanford University
  • Jurriaan Spaaks, Netherlands eScience Center

And featuring contributions from:

  • Malin Sandström, INCF
  • Alexander Struck, Humboldt University of Berlin

Introduction

The discussion session “Research Software Directories: What, Why, and How?” was held on September 16 during SORSE, an International Series of Online Research Software Events. As presenters, we each shared efforts to develop and maintain software directories: catalogues to showcase the software outputs of an institution or community. The directories presented were:

Each of the above offered several advantages and disadvantages, or were scoped for particular use cases. For example, research-software.nl provides a robust application for serving detailed metrics and metadata for software, however it requires more manual entry. The Research Software Encyclopedia is automated and does not require hosting, but it lacks the same level of metadata. The Imperial College London and GitHub Search research software directories offer much quicker to deploy solutions, but might be too simple for some use cases. The directories are discussed in detail in the following sections. In addition to this set, we suggest the reader take a look at the Awesome Registries list to find additional examples.

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Remote working for researchers and developers

This post was compiled by Mark Woodbridge, Jeremy Cohen and Tony Yang of Imperial College’s Research Software Community.

As COVID-19 drives us into uncharted territory, many of us at Imperial will be having our first ever experience of working off-campus for an extended period of time. It, of course, depends on our role, but many members of the College community will be no stranger to mobile working – pitching up at one of the many campus cafes, breakout spaces or a coffee shop, getting out our laptop or mobile device and switching very quickly into a state of focused work. Maybe finishing those next couple of paragraphs of a paper or report, fixing that annoying bug in our scientific code that someone just reported, or responding to an urgent technical query from a collaborator. Sometimes a change of space or environment provides just that little shift in perspective that you need to help solve that challenging technical problem, or get the right wording for that difficult section of the paper, much more quickly than if you’d sat in your office staring at your screen for hours!

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Running Jupyter notebooks on Imperial College’s compute cluster

We were really glad to see James Howard (NHLI, Faculty of Medicine) announcing on Twitter that he’d published a Kaggle kernel to accompany his recent publication on MR image analysis for cardiac pacemaker identification using neural networks via PyTorch and torchvision. Sharing code in this way is a great way to promote open research, enable reproducibility and encourage re-use.

Figure 3 from Cardiac Rhythm Device Identification Using Neural Networks

We thought it might be helpful to explain how to run similar notebooks on Imperial’s cluster compute service, given that it can provide some benefits while you’re developing code:

  • Your code and data remain securely on-premise, thanks to the RCS Jupyter Service and Research Data Store
  • You can run parallel interactive and non-interactive jobs that span several days, across multiple GPUs

With James’ permission we’ve lightly modified his notebook and published it in an exemplar repository alongside some instructions to run it on the compute cluster. We hope this can help others to use a combination of Conda, Jupyter and PBS in order to conduct GPU-accelerated machine learning on infrastructure managed by the College’s Research Computing Service – without incurring any cost at the point of use.

Many thanks to James Howard for sharing his notebook and reviewing our instructions

RSLondonSouthEast 2020

RSLondonSouthEast 2020, the annual gathering for Research Software Engineers based in or around London, took place on the 6th February at the Royal Society. The College was strongly represented by contributions from RSEs based at Imperial.

Full talks:

Lightning talks:

Posters:

Jeremy Cohen introduces RSLondonSouthEast 2020 at the Royal Society

Jeremy Cohen (Department of Computing) was the chair of the organising committee. Stefano Galvan (Department of Mechanical Engineering), Alex Hill (Department of Infectious Disease Epidemiology) and Jazz Mack Smith (Department of Metabolism, Digestion and Reproduction) served on the programme committee.

Many thanks to all the committee members and everyone who presented, submitted proposals or attended on the day, and to EPSRC and the Society of Research Software Engineering for their support. For more information from the event check Jeremy’s full report, RESIDE’s blog post or #RSLondonSE2020 on Twitter.

Quilting with Julia, or how to combine parallelism and derived types for high performance computing

Research and quilting have a similar Zen in that both combine and build upon multiple prior works. But the workflow is difficult to reproduce in research software: how can we combine group X’s state-of-the-art ODE solver with group Z’s state-of-the-art parallel linear algebra to create Y’s new biology model when they all use different libraries and conventions? This is the problem that Julia tackles head on, thanks to it’s innovative type system and multiple dispatch. In “Shared Memory Parallelization of Banded Block-Banded Matrices” we describe how to combine the parallelization capabilities from one package (SharedArrays) with the specialized matrix  of another (BlockBandedMatrices.jl) – without modifying the internals of either.

This work follows on from a NumFOCUS sponsored collaboration at Imperial College between the Research Computing Service and Sheehan Olver in the Department of Mathematics.

A review of the RSE team’s activities in 2019

2019 has been another very busy and productive year for the RSE team in the Research Computing Service at Imperial College. Our core mission is to accelerate the research conducted at Imperial through collaborative software development, and we have now completed 24 projects since our inception 2 years ago with 75% of our first-year projects resulting in follow-on engagements. We’ve highlighted 5 of our most fruitful collaborations on our new webpages, which also provide more information about the team and the services we offer. We are about to appoint our fifth team member, reflecting the value we’ve offered to research projects (and proving that there is a career pathway for RSEs!).

In addition to our project work we’ve assisted researchers at over 40 RCS clinics this year and played a strong supporting role in Imperial’s Research Software community, from Hacktoberfest to departmental events. We’ve developed two brand new Graduate School courses in Research Software Engineering (to be delivered next term) and have helped deliver 4 Software Carpentry workshops. We’ve also played an increasingly active role in promoting the benefits of RSE (and the role itself) to relevant stakeholders in the College. This has complemented our broader engagement activities: acting as expert reviewers for JOSS submissions, contributing to numerous OSS projects, presenting at 3 international RSE conferences (deRSE19, UKRSE19 and NL-RSE19), and promoting our work via blogging, social media and attendance at several other relevant events – locally (e.g. RSLondonSouthEast 2019) and nationally (e.g. CW19, CIUK).

RSE19 conference photograph
The team (amongst amongst many other RSEs!) at UKRSE19. Photo courtesy @RSEConUK.

We continue to develop tools and infrastructure to support RSE within in the College. The nascent Research Software Directory aims to showcase the breadth of software developed at Imperial, encouraging collaboration, re-use and citation. We’re also attempting to give software a stronger position amongst research outputs through our current work on the Research References Tracking Tool (R2T2) and helping researchers submit their software to Spiral via Symplectic. Finally, we continue to share advice and guidance on how to adopt better RSE practices, such as QA and CI.

As we look forward and further develop the Research Computing Service’s RSE capacity and expertise we’d like to thank all the academics who have trusted us with their projects, and all the researchers who’ve taken the time to explain their work and have enthusiastically embraced good software engineering practices. We’re looking forward to another 12 months of strengthening RSE at Imperial!

1st Research Software Winter Seminars and Roundtable

On Thursday 12th of December the Research Computing Service joined the College’s Research Software Community in celebrating the 1st Research Software Winter Seminars and Roundtable, the final event of another great year of building research software at Imperial. The event had two goals: first, to celebrate the research software-related achievements of the RS Community during 2019, and second, to plan the activities and goals for the year that is about to start.

The seminar session featured nine exciting talks, ranging from a review of the activities of the Community during 2019 and the training opportunities in computing and data science skills, to technical talks on the use of complex analysis pipelines for RNA sequencing and the extension of open source software with custom features.

This is the full list of talks, including several relevant links:

After the talks, there was a roundtable discussion chaired by Diego Alonso, with a panel including Elsa Angelini, Jeremy Cohen, Phoebe Pearce and Mark Woodbridge, to help answer some questions about what the audience would like to see from the Community next year, how we can communicate with each other better and who can get involved to make those things happen. There were many excellent contributions from the audience, who were also very engaged and eager to see the community grow and take an active role on it.

Among the activities that were discussed – and that gained volunteers to help make them a reality – were the creation of a Slack workspace as an instantaneous, bidirectional communication channel within the community (already up and running; sign-up now!) and the recruitment of RSE Champions in the different communities (PhD students, postdocs, etc) to promote Community events and bring more people aboard or to assist with the organisation of departmental events.

The event concluded with informal drinks and nibbles in the ICT Kitchen – including mulled wine! – where the enthusiastic attendees and speakers mingled together and shared experiences and plans for the future.

There are plenty of things going on and 2020 is due to see a very bright RS Community at Imperial!