2025 has been a big year for the Newcastle RSE team.

Let’s get the vaguely negative bits out of the way first! Like most people in the academic sector, we have had to deal with the difficulties of the current financial situation. We have also lost a few team members who have moved on to other roles.

Despite these challenges, we’ve grown to 28 members and continued to work on dozens of projects with groups across the University, as well as partners like The Alan Turing Institute and the NHS. We’ve led monthly Software Carpentry training workshops for staff and students and have been involved with the set-up of the University’s new multi-million pound High Performance Computing machine, Comet.

In this blog post, we are going to celebrate some of the team’s achievements from the last 12 months.

Research Software Maintenance Fund

Two Expression of Interest applications from the team to the highly popular SSI Research Software Maintenance Fund (RSMF) were successful, and we were subsequently invited to submit full applications to the fund. This is the first year of the fund, and it was a very competitive application process. Our full applications have now been submitted, and we are awaiting the final funding application decision from the SSI.

SSI Fellowships

In December, Mike Simpson was named as one of the 2025 Fellows of the Software Sustainability Institute, the third member of the Newcastle RSE Team to be awarded this prestigious fellowship.

Mike is continuing the conversation around mental health in the research software community. He has created the ConveRSE website to serve as a hub for mental health information and support, and has given talks at various events and institutions, including RSECon25, the Alan Turing Institute and the RSE Asia Australia Conference. Mike was also nominated for the RSE Society’s Impact Award for this work and appeared on an episode of the Code for Thought podcast.

SSI Further Development Fund

We have a number of SSI Fellows on the team, and fellows are able to apply for additional funds to continue their work.

• Jannetta Steyn was awarded £1500 to run an event: miniHPC Hackday: Building, Testing, and Sharing Best Practices.
• Dave Horsfall was also awarded additional funding to continue his work on mental health and the DIRECT (Digital Research Competencies) Framework.

The RSE Society

Mike Simpson also entered his second year as a trustee of the Society of Research Software Engineering and was elected as Vice-President. His responsibilities have included overseeing the selection process for programme chairs for future RSE conferences, overseeing the election of new trustees and overseeing the Society’s communications and outreach. Mike was nominated for the Claire Wyatt Outstanding Contribution to the RSE Community award for his trustee work.

RSECon25

We had three talks accepted to the RSE Conference at the University of Warwick this year:

• Richard Howey gave a talk on “Bridging Academia and Industry: An RSE’s Perspective on Commercial Collaboration”.
• Mike Simpson gave a talk called “ConveRSE - Let’s Talk about Mental Health”
• Jannetta Steyn gave a talk called “HPC Carpentry - An Overview of HPC Carpentry’s Activities”

Slides from the talks will be made available on the conference’s Zenodo page, and recordings of the talk will be uploaded to the Society’s YouTube Channel.

Papers and Publications

Finally, we believe that everyone who contributes to research deserves to be recognised in any publications. We also encourage the team to submit their own talks and papers to various journals and conferences.

Here are some of our success stories from this academic year.

• A paper was published in Nature based on the data collected through the app Imre Draskovits built: “Mobilising climate action with moral appeals in a smartphone-based 8-week field experiment”
• Richard Howey wrote a paper: “Bayesian network imputation methods applied to multi-omics data identify putative causal relationships in a type 2 diabetes dataset containing incomplete data”.
• Alex Surtes co-authored: “Brain morphology normative modelling platform for abnormality and centile estimation: Brain MoNoCle”.
• Becky Osselton co-authored: “A simulation study to quantitatively assess the performance of electronic prescribing systems in English NHS Hospital Trusts” as part of the ongoing NHS England project, ePrescribing Risk and Safety Evaluation (ePRaSE).

Celebrating International RSE Day 2025 was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

In the first of a series of Project Spotlights, Dr Mike Simpson discusses Colouring Cities, one of the biggest ongoing projects that the Newcastle RSE Team has been collaborating on over the last few years.

Colouring Cities

The Colouring Cities Research Programme (CCRP), managed by The Alan Turing Institute, is a research-led, free public resource, providing open spatial data on the buildings in our cities. It is an open knowledge initiative, built collectively by, and for, academia, communities, government, industry and the third sector. The programme’s overall aim is to help improve the quality, efficiency, resilience and sustainability of buildings, and urban areas, and to accelerate the move to net zero in line with United Nations Sustainable Development Goals.​​

The programme began with the Colouring London prototype in 2016 and now consists of over 150 contributors in more than 20 countries. The platform collects over 150 data fields across 12 main categories and nearly 50 subcategories, including Age, Land Use, Construction and Energy Performance. The platform allows data collection via moderated bulk upload, data streaming, and crowdsourcing, and it has started to integrate AI and machine learning tools. This data can then be explored and visualised at individual building level on an interactive map of the city.

Over the last ten years, the CCPR has expanded. The programme allows international academic institutions to co-work on a global network of interoperable open data platforms on national building stocks, and accelerate the sharing of resources and expertise.

Our Contribution

Mike has been involved with Colouring Cities for a couple of years and has made numerous contributions to the programme in that time. He has overseen the transition from the Colouring London prototype to the Colouring Core platform, which is now used by dozens of different institutions across the world. ​He has also contributed significantly to the documentation and management of the project, including overseeing the collaboration between multiple researchers and engineers all across the globe.

More Information

You can visit Colouring Britain to see the platform in action or learn more about the CCRP on the Colouring Cities website.

For more from the Newcastle University RSE Team, be sure to follow us here on Medium or on our other social media pages.

Colouring Cities was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

A quick update on the ‘ I Am Your Father ‘ blog — the story of how I became a father in lockdown — and some of my future plans…

Reminder: This blog is the work of a sleep-deprived, first-time parent, trying to talk frankly and honestly about his experience. I make no apologies for the language used.

So, it’s December 2024. We’re rapidly approaching m’boy’s fifth Christmas, and a lot has happened. Firstly, my son is still alive, and he’s at school now! It doesn’t seem like that long ago we were bringing him home from the hospital on deserted roads and holding him up like fucking Simba so that his grandparents could see him through the window.

So, why am I writing this? That is a good question. One thing that has happened over the last few years is that I’ve had some more struggles with my mental health. I’m currently still in therapy and, to be honest, I think I still have some unresolved issues (or trauma, if that’s not too melodramatic a word) from everything that happened four years ago. Learning to be a new father is hard. Learning to do so in lockdown, while dealing with questionable management decisions that put extra pressure on me at work… It led to burnout and an anxiety attack, which I didn’t really discuss with anyone.

As part of trying to process all that, I found myself revisiting the blog and the notes that I made at the time. And while yes, I struggled, and yes, I burned out, and yes, I had an anxiety attack, I think I can safely say that I handled everything remarkably well in the circumstances. Revisiting the blog has been an interesting experience that has helped me gain a new perspective.

Incidentally, if you’re interested, I’ve done some spellchecking and tidying up of the posts, but they remain almost entirely unchanged. The blog began when we broke the news to our family with Part One — The Secret and goes all the way through to Part 21 — Baby’s First (Proper) Halloween, by which point we had kept him alive for 18 months! You can read the whole series by checking out the ‘I Am Your Father’ category.

While I was doing this, I was inspired to continue with another project, which has just taken another step closer to completion…

Baby Blog - The Novel

I’ve decided that I’m going to turn the blog into a book. It’s actually an idea I’ve been working on for a while, but I only recently completed my first full draft. (Yes, I know it’s basically four years late, but I’ve had a bit on!)

The plan is to tell the story of how I became a father, starting from the night we found out that we were pregnant and going through to m’boy’s first birthday. I’ll talk about what it was like to look after a pregnant woman (in mostly normal circumstances), the buildup to — and aftermath of — the birth (and how the start of the pandemic affected it) and how we survived the first few months of learning to be new parents in lockdown.

As with the blog, I intend the book to be a frank, honest and light-hearted retelling of the story of how I became a dad, sprinkled with dark humour, the occasional word of wisdom and a whole lot of swearing. I will be including quotes from the blog, but it will mostly include new material, including untold stories and some hindsight that I’ve gained over the last four years. It will also include discussions of various mental health issues that many of us encounter in our everyday lives and that most of us encountered in one way or another during the pandemic. The tips and advice I share may not work for everyone, but if any of them can help even a single person not to have to go through what I went through, then it will be worth it.

Even if none of that applies to you, I hope that this will be an entertaining read that will give you an idea of what it is like to become a father. It is intended to be the kind of book that I wish I’d read before this all happened.

SSI Fellowship

Incidentally, this ties in neatly with some other news, which is that I have been awarded a Fellowship by the Software Sustainability Institute (SSI). My fellowship will involve me telling my story and creating a hub for resources and information to support mental health in the research software community. You can read more about it on my page on the SSI Website. Again, these resources will be aimed specifically at people working in research software, but I hope that some of them will be useful to anyone who finds them.

I’ll be posting more updates here, on the SSI website and on my various social media feeds, so follow me if your interested in updates about the Fellowship or the Baby Blog Book.

Final Thoughts

Nothing might come of this. Even if I can get the damn thing finished, it may never get published. But I’m hoping that by announcing it, I keep the momentum going.

And even if it never sees the light of day, it has been a good therapeutic exercise for me. Hopefully, I’ll have more updates for you in 2025!

Originally published at https://mdsimpson.co.uk.

As part of the celebrations, we wanted to share some of the successes of the Newcastle RSE Team and the many varied and talented RSEs who make up that team.

So, here are some of our highlights from the past year:

RSECon24

It was our privilege to once again host the eighth annual conference for Research Software Engineering here in Newcastle. #RSECon24 was also chaired by our own Dave Horsfall, who did an incredible job of making this the largest and most accessible RSECon to date.

Nature Article

Dave also had an article published in Nature. It is titled “Research Software Engineering Accelerates the Translation of Biomedical Research for Health”, and you can read it here:

• https://www.nature.com/articles/s41591-023-02353-0

Society Involvement

Mike Simpson entered his second year as a trustee of the RSE Society and was elected vice president in October. Robin Nandi also completed his second term as a trustee, having served as Society Treasurer.

Awards

Mike was also part of the team that won the top prize at the Hack Day at #CW24 (@SoftwareSaved). Read this blog post for more information about the prize-winning project Task Management for Humans as Self-care.

Talks

Team members, including Richard Howey, Gabrielle Schroeder and Mike Simpson, gave talks at various conferences.

You can read more stories from the team on our profile or follow us on social media.

Celebrating International RSE Day 2024 was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

That was the question that a team of us set about trying to answer at this year’s SSI Collaborations Workshop.

Developing software for research can be challenging. Many of us work on multiple projects simultaneously, often to tight deadlines, with world leaders in fields we know nothing about, on projects that mutate and change over time. On top of that, we have to do training, keep up with constantly evolving technologies and take on extra responsibilities to advance our careers. It will come as no surprise to most Research Software Engineers that anxiety, burnout and impostor syndrome are common in this industry.

But what can we practically do as RSEs to protect our mental health at work? We have very little control over our workloads or our salaries. And telling a burned-out engineer to do some yoga or mindfulness exercises is seldom well-received (and for good reason)! As someone who has dealt with a range of mental health issues over the last decade or so, this question is very close to my heart.

My colleague, Dave Horsfall, was granted a Fellowship by the Software Sustainability Institute (SSI) to conduct a survey into mental health in our community. I’ve been helping analyse the results, and I hope to apply for a fellowship myself to continue the conversation and help provide information, tools and support to RSEs and their colleagues.

Collaborations Workshop 2024

Which brings us to May 2024 and Day 2 of the SSI’s 14th Collaborations Workshop. We were split into groups and asked to come up with potential ideas for the Hack Day on Day 3.

We introduced ourselves and discussed our various backgrounds and interests. I mentioned my plans to apply for the fellowship, and a number of people in the group admitted to having experienced mental health issues, including neurodivergence, ADHD and anxiety. A fascinating conversation followed, including several colleagues discussing how they use so-called ‘productivity frameworks’ to help manage their workload.

Many of us were wary of such concepts, as managers often employ them to try and squeeze more work out of their (already over-worked) employees. However, our colleagues explained that using these techniques allowed them not only to be more productive but to feel more productive. They adapted these tools not to do more work for their boss but to help manage their anxiety, so they could go home at the end of the day without the nagging little voices in the back of their head telling them they hadn’t done enough.

Task Management for Humans as Self-Care

We felt that these tools could be used to help people (and RSEs in particular) work more effectively - as tools for self-care and managing their life-work balance. And so, we came up with “Task Management for Humans as Self-Care”. The idea was to create a Carpentries-style course that would introduce various tools, apps and frameworks that people could use to manage their workload. But the emphasis was on using them for your own benefit rather than your boss’s. Additionally, the idea was not that “you should adopt everything from [Framework A] or you’re doing it wrong!” The idea was to encourage people to look at the ideas suggested by each solution and adopt the ones that work for them.

We pitched the idea at the end of Day 2 and then, at the Hack Day, we started putting the course together. We were very fortunate to have qualified instructors and people who had contributed to Carpentries lessons before on our team, which allowed us to hit the ground running. While the experts set up the repository, some of us worked on writing introductory content and suggesting how the course could be structured. Others researched productivity frameworks or wrote about task management tools they had used in the past.

The course is available on the Carpentries Incubator at the link below.

Task Management for Humans as Self Care: All in One View

It’s still very much a work in progress, but what is there should give a clear indication of what we had in mind, and we hope to continue to develop it over the coming months. We focussed on the introduction and an overview of the course, and made sure that the message about it being a tool for RSEs to use for the sake of their own life/work balance and mental health was front-and-centre.

We worked away quietly once the tasks had been handed out and were so focused on our work that the judges struggled to attract our attention when they Zoomed in to check on our progress! We were then amazed and delighted when we went on to win the top prize for the ideas session and then the top prize for the Hack Day, too.

Final Thoughts

I don’t think there is a ‘magic bullet’; no single solution that can improve the mental health of everyone in the community. But projects like this - that help a subset of the community with specific problems - can make a big difference.

I also think that the fact that this project got so much attention (and won two prizes!) shows that people realise how important mental health is and that people are willing to support projects that aim to improve mental health in our community. After all, making research software more sustainable goes beyond improving our code; we have to help sustain the people writing the code, too!

Thanks to the ‘Task Management for Humans’ Team: Aman Goel, Hugo Gruson, Jez Cope, Matthew Gasgoyne, Nicky Nicolson, Olexandr Konovalov, Selina Aragon, Kirstie Whitaker, Sarah Gibson, David Horsfall.

Task Management for Humans as Self-Care was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

So, it seems a group of developers at Blizzard got sick of beating the 20-year-old dead horse of World of Warcraft and went off to form a new studio. Their goal; to make strategy games — you know, the thing that Blizzard used to be known for! They’re gonna build their own Starcraft. With blackjack. And hookers!

That game is called Stormgate, and as a huge fan of the Blizzard classics, I was eager to get my hands on it when it went into Early Access last week.

So, what is it like? And will it be able to shine in the long shadow of its lineage?

Stormgate

“Stormgate is a free-to-play, next-gen RTS [real-time strategy] set in a new science fantasy universe,” boasts the Steam Store page. It makes no boast about being developed by former Blizzard staff, but the studio’s pedigree is well-documented. IGN describe Frost Giant as a studio where “many veterans of Blizzard’s now-defunct RTS team have banded together”. Plus, apparently, there are some Command and Conquer: Red Alert 2 developers thrown in there for good measure! They announced the game a couple of years ago, and it went on to earn over 2 million dollars on Kickstarter.

Normally, all this would be a bit of a red flag for me, but it is clear that things have gone dramatically downhill at Blizzard in the last decade, and the prospect of some of those talented developers breaking free from all that and starting out on their own… I couldn’t help but get excited! All you have to do is take a look at screenshots of the game, and you will immediately be reminded of Blizzard classics, particularly Warcraft 3 and Starcraft 2. My initial suspicions were overridden, and it conjured up fantasies of a long-awaited sequel to some of my favourite games of all time.

And I’m delighted to say that, in a world where we are starved of decent, high-budget RTS games, loading up the game feels like slipping on a similar, comfy hoodie. The game’s influences are clear, and its design and mechanics are definitely familiar. But it’s not just a clone of what came before. Frost Giant have made a few tweaks, changes and innovations to the formula, which — so far, at least — seem to be good ones.

Story

Having said that, there are some things that may feel a little TOO familiar. The story — from what is available in Early Access, at any rate — is one of these areas. Blizzard has a reputation for only being able to tell one story (but at least being able to tell it well!), personified by the story of Arthas and the cursed blade Frostmourne. The game opens with a cinematic showing a mad scientist opening a mysterious portal, through which swarms a horde of demonic creatures. One man tries to shut it down, after a quick call with his daughter, Amara, but is ultimately unsuccessful. When the first level starts, it’s 20 years later, and you are playing as Amara, part of the Human Vanguard, a resistance force against the invading Infernals, who have conquered most of the planet.

And, that’s all you really get in Early Access, which is to be expected. And yes, they may be deliberately treading familiar ground to welcome players into the game and could be planning to throw some wild curveballs later on. For now, without wanting to spoil too much, my eyes rolled so hard it nearly broke my neck when a character, who looked a lot like Sarah Kerrigan, announced that she was going to spend some time studying a magic sword that looked a lot like they had just changed the colour of the LEDs in Frostmourne from blue to red!

Also, the third playable race, The Celestials, is nowhere to be seen so far, which is a shame. The campaign is what introduces you to the factions, units and abilities, and gives it all context. It’s hard to get absorbed (into what is, after all, a brand new world) without that context.

But I’m prepared to give it the benefit of the doubt. It’s a free-to-play game from a new studio that doesn’t have the huge budget that Blizzard had. You have to temper your expectations. And I’m willing to put some faith in their ability to improve the immersion and craft a more engaging story as the game moves through early access and more content becomes available.

Graphics

I have similar comments on the graphics. It has a nice art style, generally, that evokes elements of Warcraft 3 and Starcraft 2, while still distinguishing itself. It seems a little bit flat and lacking in detail compared to the higher-budget predecessors, but I don’t mind that too much.

There is currently a significant difference between the quality of the pre-rendered cinematics and the in-game models. In particular, the opening cutscene of the portal opening is gorgeous, and the characters look amazing. But then you jump into the first cutscene of the actual story and find yourself with much lower-quality and generally uglier models. Then there’s another step down to the actual in-game storytelling. There aren’t any facial animations or lip-synching on the characters, which would go a long way to making them more relatable. A huge pop-up at the start of the game does promise that this is all coming later, but it’s still a shame that this important introduction to the world and characters isn’t ready yet. I can only assume that they’re focussing on the gameplay and on starting to balance the multiplayer rather than on the single-player experience.

Given that the game is free-to-play, it’s about the level you could realistically expect. If they DO manage to squeeze some extra fidelity out of the Unreal Engine in the coming months, I won’t be disappointed, but I like what I’ve seen so far.

Gameplay

As I said, the gameplay feels pleasantly familiar, but with a few tweaks. When you get to the base-building and unit management part of the game, you start with a command centre and nearby resources that must be gathered. The humans have to train gatherer units, which travel back and forth with those resources. You have to build specific buildings to enable unit training, unlock new unit types and research upgrades. You then have to expand to other resource points on the map and then destroy your enemy. All very familiar.

But there are some twists on the formula. Unlike in War/Starcraft, you don’t have to click on an individual worker and order them to build things (and then have them stand around scratching their ass when they’ve finished!). You just go into the build menu, place the building, and one of your workers will go and build it before automatically returning to work. And, while it is possible to click on your barracks and choose which units are being trained there, you can also go to the ‘units’ menu and mash the buttons, and they’ll be added to the queue of any available building on the map. These little tweaks, on top of several quality-of-life features introduced in games like Starcraft 2, make playing the game more of a joy and less of a faff, which is something I really appreciate. (Don’t worry if you are the sort of person who likes to micromanage everything though; there are still plenty of options if you want to do that.)

I enjoyed what is available of the campaign. There seems to be some replayability, too. I replayed all of the available missions, partly because one had a branching story, where you make a choice about what to pursue next, and it locks you out of the other part of the map. Some different things happen, but the same story beats play out either way. I also found a secret that I didn’t spot the first time! I also tried cranking up the difficulty, but you can’t expect too much resistance in the first few levels of the campaign, which are basically tutorials.

It’s hard to judge based on only a handful of missions, but it’s off to a promising start and I am excited to see more of it.

Final Thoughts

On some level, I can understand why some people may be disappointed if they jump into Stormgate right now. The idea of it being a spiritual successor to some of the most beloved RTS games of all time, made by their former developers, carries a certain weight of expectation. A fact only compounded by its highly-publicised success on Kickstarter.

If, like me, you are more interested in the single-player experience, then I’d give it a while. But if you are a competitive player, then this could be a good time to get involved and help shape the future of the game.

The reality is that it’s an early-access version of a free-to-play game, being developed by a new studio that is still finding its feet. But I can see the foundations of a great game here. If you can temper your expectations, you might just find something that scratches that RTS itch. I look forward to going back and diving more into the world and the story as it moves closer to release.

Originally published at https://mdsimpson.co.uk.

Visualisations are an important tool for extracting value from data. They can also help us to tell ‘data stories’ in a way that is accessible and easy to understand.

However, many existing visualisations don’t tell the whole story; there is often additional information in a dataset that adds context or meaning to the results. But how do we include this data in the visualisation in a way that the average viewer can understand?

I have been working with Professor Nick Holliman and a number of other colleagues to explore some new ways to do this, focusing on the visualisation of uncertainty. The work has a range of potential applications and has attracted a number of interested partners, including the Alan Turing Institute, who funded the project, as well as the UK Department for Transport, local government, energy companies and even the military.

The main focus of the project has been to develop the visualisations, but we also wanted to make sure that the tools that we developed were as user-friendly as possible. Once the visualisations had been created and tested, we attempted to make them easier to use by integrating them with other applications, specifically Microsoft Power BI.

Visualising Uncertainty

We have already been collaborating with the Urban Observatory at Newcastle University to create tools to visualise urban sensor data. This data includes things like rainfall and air quality, and is collected from a number of sensors located in and around the city of Newcastle.

In order to show the results in context, we displayed the data using a series of icons (or ‘glyphs’), overlaid on a 3D model of the city, as shown below.

Here, the coloured sections of the glyphs (green circles) represent the average value reported by that sensor during the specified time period. The black and white borders around each shape are designed to help differentiate the glyph from the background and to make the colour more readable.

However, we wanted to find a way to add additional data to the visualisation, and we decided to do this by changing the way we used the white shape within the glyph.

The image below is an example of a visualisation that was produced by our tool. The visual complexity of the white shape now represents the uncertainty value. The higher the uncertainty, the more visually complex the shape becomes (i.e., the larger the number of ‘petals’ on the white ‘flower’ shape).

In this case, we were using the variance in the results from each sensor, and a high ‘uncertainty’ value may indicate a problem with that sensor or some sort of local disturbance.

This is information that would not be available to the user if only the average results were shown, as in the first image.

The Problem

The visualisations were developed using Python and Blender, an open-source 3D creation suite. To produce these visualisations, Blender, as well as the Python code and a number of other dependencies, would have to be installed onto the user’s machine. The user would then need to manually run the code that loads the data into the visualisation tool and then retrieve the resulting image(s). They would also require either a graphics card (GPU) or a powerful processor (CPU); otherwise, it can take several minutes to render these images, depending on the complexity of the models and the size of the dataset.

This is not practical for most users, so we wanted to create a more user-friendly approach that did not require the installation of any dependencies or any programming.

The Solution

We decided to investigate whether we could use another tool as a ‘front-end’, in order to make the experience more user-friendly.

We chose to do this using Power BI, which is Microsoft’s Business Intelligence tool that we have used in a number of our other projects. Power BI is capable of producing a range of interactive data visualisations using a simple and familiar drag-and-drop interface.

Step 1: Integration with Power BI (Python)

We created an API that could be given a dataset and then call Blender to render the visualisation and return the resulting image. This was successfully developed and tested using the ‘Python Visual’ option within Power BI.

This made interacting with the visualisation easier, as the user could use Power BI to specify which datasets and columns to use, as well as filter the data to produce different results.

However, several setup steps were still required to use this version of the tool, many of which required programming experience. Plus it was still necessary for the user to have Blender and the dependencies installed, and the rendering was still being done on the local machine.

So, while this was a definite improvement in usability, it didn’t solve all of our problems.

Step 2: Moving to the Cloud (TypeScript)

So, we attempted to reimplement the visual in such a way that Blender didn’t need to run on the user’s machine at all.

First, rather than using the Python Visual feature within Power BI, we decided to implement our tool as a full Custom Visual using TypeScript. This had the added bonus of giving us more customisation options within Power BI, as well as giving us access to additional information (such as how big the visual was on the screen). It also made it easier for the user to import the visual into Power BI without any programming or advanced setup steps (and meant we weren’t wasting resources rendering images that were larger than they needed to be).

The next step was to install Blender, the API and all of the dependencies on a Virtual Machine using Microsoft’s Azure Cloud Platform. This enabled us to do all of the rendering on the cloud, rather than on the user’s machine.

The diagram below shows how the various elements communicate with each other.

The Visual sends the data from Power BI to the Virtual Machine, which runs the necessary Python code and then triggers Blender to render the image. That image is then downloaded to be displayed in the visual in Power BI.

In order to provide a secure connection (as only HTTPS requests are allowed from within the Power BI Environment), an Azure Function was used as a Proxy between the Visual and the Virtual Machine.

The Result

The end result is a visualisation pipeline that is much more user-friendly than our initial tools. With this implementation, the user only needs to install Power BI and import the visual, without any additional setup, as all of the dependencies are located on the cloud. The user is able to use Power BI to set up the data and configure the visualisations in a more user-friendly way, without requiring them to even look at the application code.

While the cloud rendering process can take longer than rendering it locally (it took around 10 seconds via the cloud, compared to 8 seconds on my GPU-enabled desktop), this is a negligible delay. It also means that the image will always render in 10 seconds, regardless of whether the user is using a computer, a tablet or even a phone (assuming that they have a stable internet connection).

More

You can read more about the glyphs in this open-access paper: https://library.imaging.org/ei/articles/36/11/HVEI-206.

You can also watch a video about a project where these glyphs have been used: https://vimeo.com/901318157?share=copy

Conclusion

Sometimes, our role as RSEs is not just to provide solutions, but to find ways to make those solutions as easy as possible to use for our clients and the researchers that we are collaborating with. In this project, we successfully used Power BI to take tools that were developed for use in a lab and make them more accessible to general users.

Thanks for reading!

For more blogs from the Newcastle RSE Team, click here.

Visualising Uncertainty using Blender and Power BI was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

TL;DR;

The long version

I do love RSE Conferences, this year was my fourth. But I didn’t quite expect so much to happen in such a short time as did this year. This blog post is to serve as a story recalling the adventures of a research software engineer leading up to and attending an RSE conference and to thank all the people that made the adventure possible. Obviously I’m the hero in my own story but I would have been able to get anything done if it wasn’t for Colin Sauze, Ethan White, Samantha Finnigan, Frances Hutchings and Abhishek Dasgupta.

In the run up to the conference a few things had to happen. Since I am an SSI fellow (2022 cohort) I was still spending my fellowhip money and as part of this I decided to build a miniHPC that can be used for training. This is an extra strand to the project in addition to the other two options which is turning a Raspberry Pi into a server and also producing a flashdrive option that turns a laptop into a server, all with the purpose of delivering Carpentries workshops without access to the Internet. With these things in mind we, the CarpentriesOffline team, decided to submit abstracts to RSECon23 for a poster and a hackerthon.

I never could imagine, though, how difficult some companies make it to get educational discounts. It was impossible to get Raspberry Pi computers earlier this year so I decided to go for Rock Pi and then made the mistake of asking for an educational discount. I had three weeks before leaving for Argentina and wanted to get as far as possible with setting up the miniHPC but, alas, it took me three weeks to get an educational discount code for a next day delivery order.

Hoping to have a working HPC if our hackerthon proposal was accepted I spent the next three weeks chasing the Rock Pi order. Not one to sit still and wait, I started getting all the Pis in my house together and built a five node HPC with 4GB Pi 4s. With the help of Sam Finnigan we 3D printed a rack and cases for the Pi.

I was off to Buenos Aires for the Carpentries’ Executive Committee retreat at the time that the abstracts had to be submitted and had to rely on Colin to do the submissions. With the help of the rest of the team, Frances, Abhishek, Ethan and Samantha all was done in time.

We were quite pleased when we learnt that both our poster and a hackerthon proposal were accepted. Over the next few months we worked on our poster and the RPi miniHPC which we named Pixie. I was, eventually, able to order the Rock Pis and all the bits that were needed for the HPC. Sam and I 3D printed some more cases but I did not have enough time left to start installing software on it so it became one of the things on the list for the hackerthon attendees to do.

A couple of weeks before the conference I realised that we were suppose to deliver a two minute poster presentation. As everyone knows, things become hectic the closer you get to a conference. A two minute presentation was the last thing on my mind. Especially since I had a poster a hackerthon and a WorldWide session to organise. I knew what had to be said but I it wasn’t until the morning of the presentation that I actually sat down, typed out what I wanted to say and checked that it would fit into two minutes. That was also when I finally decided that I was going to make it a show and tell. I mentioned it before but Colin thought that two minutes would be way too little time to include a show and tell. However, I decided to go for it and placed a Raspberry Pi and the miniHPC under the desk before the presentations started.

I was pretty nervous but, as usual, once you start talking things just go as they go. I pulled out the RPi, then showed the flashdrive and finally brought out the miniHPC. At the time I couldn’t quite sense how things went because the session chair had stood up which meant I had 30 seconds and I was focused on finishing and getting back to my chair. But once the session was over my colleagues seemed pretty pleased and loads of people came up to ask questions. Phew!! That was Tuesday.

Wednesday started with the hackerthon. We had worksheets prepared and printed (thank you Frances) as we knew what had to be done but just how we would go about it all was difficult to decide on. So I think, we pretty much played it by ear. We told people what the things were they could work on and then they divided themselves into groups trying to work on those things. I hope participants weren’t too disappointed. At least they managed to get hands on experience with everything that can go wrong when you work with a project like this. The time we had was a bit short but as long as their experiences made it into the documentation their efforts will help us a great deal.

This year I was a member of the RSE Conference committee and I was co-chair for the WorldWide session which was scheduled for the Wednesday afternoon. Unfortunately, half-way through the session I received an urgent call from a colleague whom I then had to escort to A&E where I spent the night to keep her company. Fortunately, all turned out fine and we are all okay. Except that Thursday morning I decided to do a Covid test … and guess what? No good deed goes unpunished! I tested positive.

At least I was able to watch the awards session on Zoom and it was a great honour to learn that we received the best poster award and that I was chosen to receive the RSE Community award for Training and Education. My manager accepted the awards on my behalf but he did a very bad job of looking like me. Note to manager: I’m short and chubby not tall and handsome!

This brings me to the point where I have to thank everyone involved that led to me receiving these awards. I mentioned everyone involved in creating the poster but they are also the people who have been putting a great deal of work into CarpentriesOffline. With regards to the Training and Education award I obviously could not do this on my own. I have to thank the wonderful Carpentries and RSE communities, which include my colleagues, for their support and their infectious enthusiasm. I have to thank the Software Sustainability Institute for the support and funding to work on CarpentriesOffline and the RSE Society and its community for recognising our efforts and providing an environment where we can share our thoughts and ideas with like minded people while having fun doing our jobs.

Originally published at https://www.jannetta.com on September 18, 2023.

CarpentriesOffline at RSECon23 was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

As Carpentries ( carpentries.org) instructors probably know, sticky notes are important in our teaching. Although we are now addressing the selection of sticky note colours as an issue for people with colour vision deficiencies, traditionally a green sticky on a learners screen would mean the learner is okay, or they finished with the exercise given, while the red sticky means “I need help!”. As someone said to me: “You can’t type with one hand”, so rather than sitting with one hand in the air, with the help of the red sticky, at least you can carry on working while waiting for help to arrive.

We need our stickies. But, and I don’t know if it is only here in the UK, the stickies I buy here won’t stick. They keep falling of the screen which means they are more of a distraction than help and for this reason I have been trying to come up with an alternative solution for quite some time now. I do usually end up handing out Blu Tack [1], but that’s just wrong; sticky notes, as the name implies, should stick! Also, at the end of every class, I am always left feeling pretty guilty when having to collect and throw away a lot of wasted paper. We all know that ducttape fixes everything and I believe my 3D printer goes with everything that needs to be fixed — I had an idea. As usual, my bright ideas hit me the night before when I do not have much time left to implement it. In the six hours that were left of the day after getting back from the office I implemented this solution:

I used OpenSCAD to design two round discs, one with a cross and one with a tick mark. I printed these discs with red for the cross and green for the tick on a white background. My thinking was that for people with normal vision the red and green is helpful and for those with colour vision difficulties the colour wouldn’t matter because the contrast of green and red on white is quite significant. Because the cross and tick are quite distinct, even in black and white it should be clear what the difference is. I designed the discs such that they can be mounted on kebab sticks and attached to the side of any monitor with Blu Tack. I have addressed quite a few issues with this option:

1. Colour vision deficiencies are addressed
2. No more paper waste and for those that use the stickies to get feedback — you can use a whiteboard or a collaborative document (or one of several alternative online options)
3. Printed from plastic the discs are reusable and should last for quite a long time
4. The plastic I used for printing is recycled PLA (from Filamentive) which can be recycled again
5. The kebab sticks are wood, thus biodegradable

It takes about 2.5 hours to print 12 discs, which have to be glued together, back-to-back, giving you 6 sticks. So a bit time-consuming and tedious but doable — even the night before the workshop.

In their feedback the learners indicated that the sticks worked well so I think they will serve as a good replacement for stickies that won’t stick. I will be uploading the OpenSCAD and STL files to printables.com [2]. If you don’t have access to a 3D printer or a 3D printing service, do give me a shout. Time permitting and at a cost to cover my expenses and postage I might be able to print for you.

• [1] Adhesive Putty, Mounting Putty, Sticky Tack, Prestik
• [2] https://www.printables.com/model/530980-tick-and-cross-sticks-for-teaching

Originally published at https://www.jannetta.com on July 19, 2023.

When The Stickies Won’t Stick, Use Sticks was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Every year, the Software Sustainability Institute hosts the Collaborations Workshop, an event bringing together all kinds of people from across the UK and beyond to explore ideas around software and research.

This year, I attended my first CW, and I thought I’d take some time to write about my experience. What was it like? How does it differ from other events? Would I recommend it? Read on to find out!

First, some context:

The Software Sustainability Institute (SSI) has been trying to cultivate better, more sustainable research software since 2010. Their slogan: “Better Software, Better Research”, neatly summarises their goals (and you’ll rarely meet an RSE whose laptop is not adorned with stickers bearing that slogan!).

The Collaborations Workshops (CW) have been running for fifteen years, with the first taking place in 2009. As quoted on their website: “CW brings together researchers, software developers, managers, funders and more to explore important ideas in software and research and to plant the seeds of interdisciplinary collaborations.” CW23 was the first in-person CW since 2019, as well as the first hybrid event.

It was also my first CW, so I went into it not really knowing what to expect. I’m used to regular conferences, which mainly involve listening to other people talk — don’t get me wrong, I’ve watched some great talks — but this was different. So I was excited and more than a little nervous to see how it would play out.

Day 1

We arrived at the hotel to find a familiar welcome: registration, followed by coffee and a quick catch-up with familiar faces from the RSE Community. There was then an introduction to the workshop and the SSI, along with some tips for getting the most out of the event. We were also set a challenge: talk to at least seven new people during the workshop!

There was then a fascinating panel with senior members of the community, discussing career paths. The key takeaway was that a career can look impressive when you put it on paper in chronological order. It suggests that there was a clear plan that was being followed. However, the reality is, more often than not, a lot more chaotic and improvised (which was a reassuring thing to hear from these very successful people with impressive CVs!).

We then listened to a handful of lightning talks, many of which were setting up ideas for the Hack Day or just trying to start conversations about important topics.

A great start, though so far, it felt a lot like a traditional conference.

However, after a group photo and lunch, we entered the first Discussion Session. Our topic: “What resources, support and pathways are available for developing your career as an RSE?” It was an interesting discussion about a topic that I have pretty strong opinions about, and it was both edifying and unsurprising to see that other people feel the same way. We didn’t just focus on the negatives, however, and were able to share a few tips and resources with each other, which was great.

I missed part of the afternoon session because I wasn’t feeling well (I’m still recovering from going on holiday with a toddler!). However, I’ve heard nothing but good things from colleagues who attended the first set of mini-workshops.

By the evening, I was feeling better and was able to attend the drinks reception and dinner, which took place in the Manchester Museum. We were assigned tables for dinner, which gave us another chance to talk to some new faces, and it was a delightful evening; eating, drinking and chatting while surrounded by dinosaur bones, taxidermied animals of varying levels of quality, and the suspended whale skeleton in the Living Worlds gallery.

It was a long day but an interesting and enjoyable one.

Day 2

The next day opened with more mini-workshops. I found myself discussing the challenges of managing software projects in academia. How do you manage projects with such an extensive range of scales, participants and flexibility in how they play out? Are certain approaches (such as Agile) appropriate for use in RSE projects? I’m not sure we found any concrete answers, but it was certainly a fascinating discussion.

We then had a ‘Collaborative Ideas session’, where we were put into groups and encouraged to come up with an idea, either something for the Hack Day or something that would benefit the research software community. I floated an idea for continuing to support mental health within the community, based on the work of colleague and SSI Fellow Dave Horsfall, as that is something very dear to me. However, I didn’t have a concrete plan, and so I was more than happy to work with everyone else on another idea called ‘Code Orchard’. We thought it would be useful to create resources for people who want to teach software engineering and data science, similar to the Software Carpentries but aimed at school-aged children. We wanted to promote the idea of solving problems and altruism through coding, to encourage more people, especially young women, to get into the world of coding and research.

Our idea went on to win second prize, following a vote by our fellow delegates, and I hope is something that we can pursue further in the future.

There then followed some more interesting Lightning Talks and another mini-workshop session on Champion Programmes (like the SSI Fellowship), including how useful they are to the Champions and their careers, and what more can be done to improve these programmes moving forward.

That evening, there was a buffet dinner at the venue, which gave me a chance to rack up my ‘new people talked to’ count, and gave me an opportunity to discuss some ideas I had for my own SSI fellowship application, which I am considering for later in the year.

Day 3

Unfortunately, I couldn’t stay for Day 3 of the Workshop, which was Hack Day. The idea was to get into teams and try to create prototypes or develop some of the ideas that had been suggested beforehand, or came up in the sessions/conversations that took place over the first couple of days.

My colleagues who were able to attend said that it was a challenging but rewarding experience, and I hope to be able to stay for the Hack Day at future workshops.

Final Thoughts

So, that was my first experience of the SSI Collaborations Workshop.

I have to admit that I was slightly nervous about it. However, I am delighted to report that it was a welcoming atmosphere, everyone was so friendly, and I certainly felt included.

In general, it felt like a very inclusive event, not only for those who were there in person but — from what I could tell — for those who were joining remotely too. I know how difficult it can be to not only livestream the sessions but make it a worthwhile experience for online participants. It was not without its technical problems, but I thought it went surprisingly well, given that it was the first hybrid event (and, as a committee member for the RSE Conference in September, I was definitely taking notes!).

All in all, it was a fascinating and rewarding experience. I got a lot out of it personally, and if even a tiny percentage of the ideas and conversations that took place develop into anything, then I think the whole community will greatly benefit from it as well.

See you at CW24!

CW23: My First Collaborations Workshop was originally published in Newcastle University Research Software Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.