Introduction

The core goal of my SSI Fellowship is to facilitate knowledge exchange of skills and competencies between humanities and sciences. This includes improving my own knowledge and skills relating to the latest AI techniques and their relevance for teaching and learning.

In November 2025, I attended the ELIXIR BioHackathon Europe event at Bad Saarow near Berlin, Germany. The BioHackathon runs every year thanks to ELIXIR Europe and provides space for collaboration and innovation in computational biology and bioinformatics. Participants engage in intensive, hands-on programming and content-creation activities, data integration and software development. I joined the project ”Knowledge graphs for metadata on training”, led by Geert van Geest (SIB Swiss Institute of Bioinformatics), Harshita Gupta (SciLifeLab Sweden), and Vincent Emonet (SIB).

Outputs, report and user stories

The project has published a report of its outcomes on BioHackrXiv [precise link and citation to follow]. Highlights of the report include:

• A description of what a knowledge graph is, and how this structured data representation can greatly facilitate complex querying and applications to deep learning approaches like generative AI.
• A description of the training registry metadata sources we used (TeSS and Galaxy Training Network) and the most important metadata fields.
• A description of the code written to build the knowledge graph, and Model Context Protocol (MCP) server we developed that exposes a suite of tools for searching and querying training materials. 

Several projects at the BioHackathon featured Model Context Protocol (MCP), and this was a new concept for me. MCP is an open standard produced by Anthropic (the company responsible for Claude); think of it as a more powerful kind of API. An MCP server gives AI agents a consistent way to connect with data, tools and services, while reducing hallucination. Agents can perform multi-step tasks, reducing the effort for the user who can interact via a natural language interface. For us, we can present a LLM chat bot that can query multiple training registries at once and provide answers to much deeper questions.

When I applied to this project, I had intended to work on the Python code directly. In the end, I changed my focus to provide project and community management. My most significant contribution to the project was to lead the development of 11 user stories. These user stories are a representative selection of the kinds of queries a user might make of the system, following a popular format:

• As a [user persona]
• I want to [do task]
• …so that [outcome/benefit]

An example user story we created is:

• As a bioinformatics scientist
• I want to define a learning path of training materials and/or events
• …so that I can become a specialist in artificial intelligence within the following specified time and resources: I have 6 months, a workload of 14 days, I live in Sweden and I can travel within Europe once.

Having a range of user stories ready to refer to throughout the project helps the developers to keep the requirements in mind when coding and allows them to focus on the software development.

Impact and opportunities

The project was a successful creation of a proof-of-concept for the ELIXIR ecosystem and beyond. There is a promising possibility of MCP for scientific applications, where used in combination with a LLM, to allow for natural language querying while including information from a trusted resource.

Participating in the BioHackathon gave me a better appreciation of current AI applications and features, in turn supporting me in my core work and with other aspects of my SSI Fellowship. I learned more about the importance of having persistent, unique identifiers for all nodes in a knowledge graph, and how it is valuable for various concepts described within the source materials to be described with an ID. The knowledge graph we built had gaps which had to be filled afterwards, and it would be more accurate if these gaps were already filled by the training providers before we scraped the training materials. We already associate the URL of a training course or event as the unique identifier for the material as a whole, but what about the trainers, the hosts and the locations of events? There are recommended authorities to consider, such as ORCiD for persons, ROR for organisations, and Open Street Map for places. I can now advocate for training registries and providers to host additional metadata for these inner entities within a given training material.

Thank you to the project leaders Geert van Geest, Harshita Gupta, Vincent Emonet, and all the other project members Finn Bacall, Jerven Bolleman, Jacobo Miranda, Dimitris Panouris. Thank you also to the people who kindly helped answer my questions during the hackathon: Alex Botzki, Eli Chadwick, Alban Gaignard, Helena Schnitzer, Ginger Tseung, Bérénice Batut, Carole Goble.

Figure 1. Scientific fields converging on computer-vision-based methods for quantifying behaviour. Deep-learning approaches extract user-defined body parts directly from video without markers, enabling high-throughput, non-invasive motion tracking across species.

Overview

Niko Sirmpilatze is a 2025 Software Sustainability Institute (SSI) Fellow and Senior Research Software Engineer at the Sainsbury Wellcome Centre, a neuroscience research institute affiliated with UCL in London. He builds open-source tools to study brains and the behaviours they produce, and leads movement—a Python package for analysing animal motion.

I organised the first Animals in Motion workshop in London, which was the central goal of my Software Sustainability Institute (SSI) Fellowship. The event brought together early-career researchers from diverse disciplines, all united by a shared aim: quantifying animal behaviour using open-source software.

Animals in Motion formed part of a broader Open Software Week held on 11–15 August 2025, which I co-organised with SSI Fellow Alessandro Felder, supported by many of our colleagues at the Neuroinformatics Unit. You can read more about the wider week in this companion post, where Alessandro and I reflect on the added value of combining our Fellowship activities.

In this post, I share highlights from the Animals in Motion workshop, reflect on what we achieved, and outline what comes next. Throughout, I use “we” to refer to the full team behind Animals in Motion—including Sofía Miñano and Chang Huan Lo, who were instrumental in designing, developing, and delivering the workshop materials.

Fellowship goals

When proposing my Fellowship project, I argued that several scientific fields interested in animal behaviour—from neuroscience to behavioural ecology—are converging on shared, computer-vision-based methods for measuring motion. Thanks to advances in machine learning, researchers can now track body movements directly from video, at scale and low cost (see Figure 1).

I saw this convergence as an opportunity to bring together researchers from these diverse communities and train them in using sustainable, open-source tools that support their common workflows. The goal was to build bridges between these communities and to create a two-way exchange between researchers and tool developers:

• Researchers would gain theoretical grounding, practical skills, and a new peer network.
• Tool developers (including the organising team) would learn from real users, building relationships and gathering feedback to guide future work.

By blurring the lines between these groups we hoped to consolidate and strengthen the shared ecosystem of open tools for behavioural analysis.

Workshop attendees

We promoted Animals in Motion widely across social media, mailing lists, online communities, and Slack channels, as well as through targeted outreach to graduate programmes and institutes focused on animal behaviour. As this was the first event of its kind, we were unsure how much interest it would attract. The response exceeded all expectations: we received 60 applications from around the world, most of them of high quality.

We selected 25 participants, the maximum number we could accommodate for hands-on teaching, and were delighted that 24/25 attended both workshop days—dispelling our concerns about potential no-shows. Thanks to support from the SSI and our other funders—described in the companion post about the Open Software Week post—we were able to charge no registration fees, provide catering for all, as well as fund travel for four Animals in Motion attendees. This helped us achieve strong geographic diversity: 9 attendees from London, 7 from the rest of the UK, 6 from Europe, and 2 from India.

We succeeded in bringing together diverse disciplines, species, and experience levels. Based on an opening poll (Figure 2), we welcomed researchers working with animals ranging from mice to… “flying” frogs—and spanning fields including neuroscience, behavioural ecology, biomechanics and conservation. Career stages ranged from Master’s students to early-career principal investigators. Two-thirds of attendees identified as women, likely reflecting the underlying demographics in these fields.

Figure 2. Word clouds generated using mentimeter.com show the range of scientific disciplines and model species across attendees.

From both direct observation and participant feedback, this mix of varied backgrounds and shared technical interests worked extremely well. Engagement levels remained high throughout the workshop and participants felt enriched by the diversity of attendees.

Workshop content

We began the workshop with a primer on deep learning for computer vision, in which Sofía Miñano introduced the concepts and technologies that underpin modern animal tracking tools. Several participants appreciated the accessible introduction to what can often feel like a complex and opaque field.

In the afternoon, we switched to practical training with SLEAP, using materials prepared by Chang Huan Lo. Participants learned how to annotate videos, train computer vision models, and use them to track animals. We provided sample videos to ensure everyone could follow along, although some people experimented with their own data, resulting in a fun showcase of diverse animals.

Day two focused on analysing motion tracking data using our open-source Python package movement. Participants worked through exercises that introduced them to loading, cleaning and visualising data, as well as asking questions about the animals’ kinematics. We finished with two real-world case studies that demonstrated how the tools covered in the course support ongoing scientific research.

Catering to the wide range of coding experience among attendees proved to be a challenge, especially during the Python-heavy second day. We had offered an optional introductory Python session before the workshop, but that could only go so far. To address this, we encouraged more experienced coders to support classmates, which had the added benefit of contributing to a strong sense of community.

Participants told us they would have appreciated even more time for exercises and discussion, and that is something we are keen to build into future editions. It was also extremely rewarding and useful to see our movement package in action, crash-tested in the hands of so many users.

We have chosen to openly share all workshop materials in the Animals in Motion Online Handbook. The handbook contains chapters written by Sofía, Chang Huan and myself, and it can be followed independently as a self-paced resource. We intend to keep expanding and updating it in response to feedback gathered during the workshop, so that it remains a freely accessible and reusable teaching tool for the community.

Blurring the lines between users and developers

A healthy open-source ecosystem relies on helping users become contributors. Hence a key aim of my SSI Fellowship was to give animal behaviour researchers the skills and confidence to take that step.

The Hackday, held on the final day of Open Software Week, was our main way of putting this into practice. About half of the Animals in Motion participants stayed on, joining attendees from other tracks of the week. To help everyone get started, we preceded the hackday with an optional half-day workshop on Collaborative coding with git, delivered by Joe Ziminksi and Laura Porta.

The hackathon itself followed a format inspired by the SSI Collaborations Workshops. You can browse the projects on this board. Some teams explored open-source tools using their own data, while others made contributions upstream—including several pull requests to movement, two of which have already been merged. One participant, Carlo Castoldi, also wrote a blogpost about his contribution, published on the movement website.

I will take this opportunity to especially thank Sofía Miñano, who proposed no less than five project ideas, mentored multiple teams during and after the hackday, and helped Carlo with finalising his contribution. She was the true hackday hero.

What's next

Organising and leading Animals in Motion has been the most rewarding experience of my professional career. I’d had ideas like this floating around for some time, but the SSI Fellowship was the catalyst that turned them into something real. The process of articulating those ideas for the Fellowship helped give them structure, and feedback from colleagues—as well as from my SSI mentor Colin Sauze—further refined them into a concrete plan.

I’m excited to keep building on this work. It’s been wonderful to see Animals in Motion so warmly supported by my team and our host institute. Animals in Motion will return on 17–21 August 2026, as part of the Neuroinformatics Unit Open Software Summer School—an event we aim to make an annual tradition.

My hope is for the workshop, alongside its online handbook, to form the nucleus of a growing community of practice for open-source tools in animal behaviour. In the long run, I’d love to see other teams around the world running their own versions of the workshop, building on the open materials we’ve created. If you would be interested in supporting such an effort, I'd love to hear from you. You can find my contacts through nikosirmpilatze.com.

Alessandro Felder is a 2025 SSI fellow and a Senior Research Software Engineer in the Neuroinformatics Unit (NIU) and in the Advanced Research Computing Centre at University College London. He is a core developer of the BrainGlobe Initiative, an open-source suite of tools to process, analyse and visualise brain microscopy data. He is also active in local and international community-building activities in bioimage analysis.

In this blog, I share the motivation for applying to the SSI fellowship programme, what the contents of my fellowship event were, what I’ve learnt during my fellowship, and how I think my fellowship activities fit into the wider landscape.

My fellowship event consisted of two "tracks" that formed part of Neuroinformatics Open Software Week—a larger event that I co-led with my colleague Niko Sirmpilatze (also a 2025 SSI fellow). I am deeply grateful to him and my other NIU colleagues for their support in making our vision into a reality. You can read our joint blog to know more about how we coordinated our fellowships, and our overall conclusions.

I would also like to thank my SSI mentor Richard Abel, who gave me some particularly helpful advice around how my fellowship could fit into my wider career plans.

Motivation—The Missing Bridge

I’ve spent the past decade of my professional life (as a PhD student, postdoc and then “official” Research Software Engineer) working at the interface between biological image analysis and research software engineering—both are fields that I have grown to care deeply about, and I like to share this enthusiasm with others.

During this time, I noticed various similarities in the community efforts in both fields: Research Software Engineers and Bioimage Analysts both see themselves as performing critical and underappreciated technical roles in the interest of scientific progress that lack appropriate career paths. The self-reported activities of a recent survey of bioimage analysts (see Supplementary Figure 1B of the preprint) overlap significantly with "the mixture of service delivery, research, innovation and teaching activities" cited in the job descriptions of generalist research technology professionals at UCL (e.g. for RSEs). There is even a recent paper which advocates for embedding software engineers in imaging facilities.

Despite these similarities, I was not aware of community initiatives that linked the two fields. I decided that an SSI fellowship event could help bridge the communities—in the hope that jointly advocating for recognition of technical roles in academia might result in better career paths for both.

As someone that works with whole-brain microscopy data, I was also aware that advances in imaging techniques mean imaging data is getting bigger, and that we need software that keeps pace with these developments. I also realised how important the perspective of bioimage analysts (here meaning anyone with a need to analyse imaging data, such as microscopy facility staff and early career researchers) is in addressing these software challenges. This was yet another reason to connect the specialist bioimage analysts with more generalist research software engineers.

One very awkward self-tape and an afternoon of interactions with amazingly collaborative people later, I was happy to find out that I was awarded the fellowship… and the real work began.

As I was planning the event, I decided to divide my fellowship event into a whole-brain microscopy data part, the BrainGlobe track, and a more general Big Imaging Data track with a focus on community and file formats. Participants could join just one track, or both.

BrainGlobe

In the BrainGlobe track, we strongly favoured applications where there was evidence for a clear immediate use for the BrainGlobe tools. We selected 15 applicants from around 50 applications—eight were based in London or Surrey, four were based in Europe and three came from further away (Singapore, USA, Australia).

The event itself consisted of hands-on BrainGlobe tutorials, a suite of open-source software tools for neuroanatomy I co-develop. BrainGlobe helps researchers process, analyse and visualise their brain microscopy data—an important datatype for my institute and a key application driving the need for software that can handle big imaging data. Participants were encouraged to bring their own data along. Fellow BrainGlobe core developer Igor Tatarnikov also helped a lot with this and led some of the teaching itself.

We were impressed with the level of preparation of the participants: many had brought their own data and detailed questions— and this led to the event being more of a two-way learning experience than we expected: we took note of 13 issues, mostly related to user experience or unusual setups, that we weren’t aware of. Two attendees went a step further and contributed improvements to BrainGlobe since attending.

We found this experience rewarding and highlighted the importance of a continued dialogue between users and developers.

Big Imaging Data

We selected 23 applications for the Big Imaging Data track—19 made it, with eleven attendees from outside the UK showing the global reach of the participants. Again, we were quite selective with the applications (we had space for 25 participants). I was particularly pleased to welcome four imaging facility staff, who I see as an integral part of the community because their role often includes training researchers on acquiring and analysing big imaging data.

The morning included an introduction and a hands-on tutorial around OME-Zarr, the "next-gen" community-centred big imaging data format. Designing these materials, I relied heavily on the open-source OME-Zarr for Big Bioimaging Data textbook, led by my colleague David Stansby and invited textbook co-authors Kimberly Meechan and Ruaridh Gollifer to present their work about benchmarking OME-Zarr libraries—thank you! I learnt a lot from them, and from designing the tutorial—a major take-away was that despite community support and a clear need for OME-Zarr, much of the software ecosystem around it is rather fragmented and immature, and more work needs to be done here.

In the afternoon, I introduced my personal perspective on the missing interactions between the bioimaging community and the RSE community—which was my motivation for applying for an SSI fellowship. We then transitioned into a speed-blogging session: I invited participants to discuss a related topic of choice in a small group and then write this up as a blog. I provided some possible topics as a prompt, but participants were free to come up with their own. This resulted in four blogs (in preparation), which centred around career paths, the notion of open science, guidelines for using OME-Zarr and bridging communities.

I was very inspired by the level of buy-in from all participants, especially for the speed-blogging session and I am excited to see our blogs published. Going beyond learning technical skills and into community building was an important part of my plans— and while the community-building aspect was built-in throughout Open Software Week, this part let us explicitly think about and imagine the communities we want to be part of.

It was also great to see an OME-Zarr-related hackday project. We started writing jupyter notebooks that showed how different libraries can be used to convert datasets to OME-Zarr.

The bigger picture

My hope is that my fellowship event was a small step in coordinating technical development and career paths in both fields. I believe it was a timely step, too: for example, the Global Bioimage Analysts' Society is aiming to include software developers in their scientific advisory committee.

My fellowship made me realise how interested I am in seeing where domain specialists and generalists meet, and how this helps drive research forward. I see this as a key area of growth for the Research Software Engineering movement, and we need to find solutions to include more people from domain-specific backgrounds.

Leading this event also helped me become more visible in my communities—alongside my SSI fellowship, I have helped organise the upcoming Crick Bioimage Analysis Symposium, which will feature a panel discussion around software sustainability and funding (kindly supported by the RSE Society) and I am also involved in organising the data session of a university-wide bioimaging conference. Finally, BrainGlobe was recognised with an Open Science prize recently.

I look forward to the next iteration of the BrainGlobe and Big Imaging data tracks next year!

Alessandro Felder and Niko Sirmpilatze are both 2025 SSI Fellows and Senior Research Software Engineers at the Sainsbury Wellcome Centre, a neuroscience research institute affiliated with UCL in London. Alessandro is a core developer of the BrainGlobe Initiative, an open-source suite of tools for processing and visualising brain microscopy data. Niko leads movement, an open-source Python package for analysing animal body movements from video.

Overview

In August 2025, we co-organised the Neuroinformatics Unit Open Software Week (OSW) a five-day event that brought together 44 attendees from 12 countries across four continents to learn open-source approaches for handling large imaging datasets, processing whole-brain microscopy data, and analysing behavioural videos. OSW emerged by combining our SSI Fellowship plans into a single, larger initiative.

Across the week, 13 speakers delivered seven sessions, grouped into three main tracks supported by four shared satellite events:

Schedule of the Neuroinformatics Unit Open Software Week.

Main tracks

• Animals in Motion focused on open-source tools for tracking and analysing animal motion from video.
• BrainGlobe consisted of a hands-on introduction to open-source tools to process, analyse and visualise brain microscopy data.
• Big Imaging Data featured introductory technical tutorials and a community session around big imaging data formats and libraries.

Animals in Motion was led by Niko, while the other two tracks were led by Alessandro.

Shared satellite events

• Introduction to Python — optional one-day refresher for participants wanting to strengthen their programming foundations ahead of the technical sessions.
• Careers Clinic — a panel discussion with five Research Technology Professionals from life sciences, highlighting diverse career routes and opportunities.
• Collaborative Coding with Git — practical guidance on version control and contributing to projects on GitHub.
• Hackday — a dedicated day for participants to collaborate on small projects, drawing inspiration from the SSI’s Collaborations Workshops.

The programme was supplemented by a series of diverse social events in the evenings, including a walk in the Regents Park, an Irish folk music jam session, a neuroscience-themed pub quiz, and a creative live-coding evening.

In the two companion blog posts, we describe the individual training tracks we led and how they helped advance our respective Fellowship goals.

• Bridging communities around big imaging data for brain microscopy and beyond

• Animals in Motion: empowering behavioural researchers with open-source tools

In this post, we reflect on the experience of joining forces to achieve something more ambitious than either of us originally envisioned. We share how the event came together, the synergies that shaped it, and our plans for the future.

Synergistic fellowships

Open Software Week wasn’t part of our original plan. We had each proposed independent Fellowship projects and were simply lucky that both were funded in the same cohort. The idea to combine them came to us later. It made sense — we work side by side at the same institute and had already planned to use the same spaces for our respective events. We expected that we could combine some parts of our events, such as the hackday, and share the logistical and administrative burden. To our surprise, joining forces came with other unforeseen benefits, too!

We didn't expect how much working together would help us when we needed someone to bounce ideas off, or someone to hold us accountable for getting things done (including writing this blog post!).

We also benefited from each others' and our line manager Adam Tyson's perspective as we reviewed an overwhelming amount (~120) of high-quality applications. We were limited to 50 participants - the maximum number we could teach hands-on in our space. It was a lot easier to make tough decisions together. It helped that Niko wasn't as emotionally close to Alessandro's plans, and vice-versa. Adam could tie-break and keep a higher-level perspective.

Making our fellowships into a larger event with existing seed-funding allowed Adam to secure additional sponsorship for OSW. We got small grants from the Society for Research Software Engineering and AIBIO-UK, as well as support from our host institute. The Sainsbury Wellcome Centre provided funding for OSW in addition to their already generous in-kind contribution of administrative support and provision of teaching rooms. This enabled us to provide catering throughout the week, not charge registration fees and support eight participants with accommodation and travel costs.

Attending tracks on different topics did not prevent our participants from making friends during the shared breaks and social events. The boundaries between our events were fluid and we were happy to see many engaging interactions: a participant switched tracks at the last minute, an Animals in Motion attendee helped with BrainGlobe problems during the hackday, and a few participants took time out of the Big Imaging Data event to attend the Careers Clinic.

Although OSW grew out of our SSI Fellowship initiatives, it was quickly and enthusiastically adopted by our fellow research software engineers in the Neuroinformatics Unit. A final positive outcome was that organising and leading OSW (it was pretty intense, to be honest!) brought us closer together as a team. The end of the week found us having tea and biscuits together, exchanging stories and cooling down from all the excitement.

What made Open Software Week a success

OSW was rewarding and worthwhile for us organisers, and we hoped that the participants would share this experience. Gratifyingly we received overwhelmingly positive feedback; we've included some anonymous excerpts below.

Sparked a bit of a eureka moment after months of agonising over how to analyse my data!

My whole PhD feels doable now!

The heterogeneity of the attendees was truly enriching.

Atmosphere was very friendly and down to earth.

The communication and offers of help were incredibly kind and respectful. I felt uninhibited to ask questions, which I don't take for granted!

It was incredibly valuable to learn directly from the developers and share the space with researchers from across the field.

I thought the motivations behind the week and the organising team were eye-opening as to how to make a career supporting research and doing this type of work. I didn't expect to feel as welcomed and motivated to keep going in this field…

Moreover, we had little to no decline in participation as the week progressed. Attendees, including the locals, kept showing up for all the days they'd signed up for. Many of them remain engaged on our public discussion forums and some have already contributed multiple times to our open-source tools. One of our participants, Marco Dalla Vecchia, wrote a first-hand account of his experience, which you can read on the Neuroinformatics Unit website.

We have been reflecting on what made this event such a success.

One factor that stood out was our model of combining domain-specific data analysis training with general good research and software practices. Because participants were already motivated to learn skills they could immediately apply in their own work, they were more engaged and receptive to topics that can otherwise seem dry, such as version control or introductory Python. We think this integrated approach may be more effective than teaching software skills in isolation. Our selection process also reinforced this, as we prioritised applicants who were likely to make immediate use of the tools and methods covered.

We also made a concerted effort to create a welcoming and informal atmosphere, using techniques from SSI Collaborations Workshops and other communities with a similar ethos—like Brainhack. Each day started with a welcome session, where everyone was reminded to follow the Code of Conduct, be collaborative and respectful, make friends and have fun. We encouraged participants to follow the Pacman rule and tried to lead by example on that. We also made sure to include unconference-type sessions with participant-led co-working activities and provided an online platform for people to chat during the event.

Looking ahead

We plan to build on the success of OSW by growing it into an annual summer school. Next year's event is scheduled for August 17th-28th 2026 and registration opened on December 1st 2025.

We aim to expand the programme to two weeks. This will allow us to introduce a dedicated additional track on electrophysiological data, an important neuroscientific modality that was missing in 2025. The 2026 event will also provide more opportunities for participants to present their work and have more time for collaboration.

To ensure long-term sustainability, we will shift to a mixed funding model that combines sponsorship with registration fees, while continuing to offer travel support for participants from under-resourced institutions and countries.

We are excited to host our next cohort in London next summer!

Acknowledgments

Looking back, OSW feels like the most impactful initiative we have undertaken so far. Experiencing how our efforts helped connect researchers across disciplines and career stages was deeply fulfilling. We are grateful to everyone who helped transform our initial fellowship ideas into something far greater.

We wish to thank all of our colleagues in the Neuroinformatics Unit. Shout-out to Adam, Chang Huan, Igor, Joe, Laura and Sofía, who all contributed in multiple ways, from developing and delivering training materials, to organising social activities and leading hackday projects.

OSW would not have taken place without the generous funding from the SSI, the Sainsbury Wellcome Centre, the Society for Research Software Engineering and AIBIO-UK. The finance teams at SSI and the Sainsbury Wellcome Centre also helped streamline the admin and ensured we never had to cover costs out-of-pocket. Our Events Manager Karen Fergus was instrumental in arranging room bookings and, crucially, managing travel and reimbursements for the eight stipend recipients. The food provided by the catering team received frequent praise in participant feedback, and the security team supported us with room set-up and access throughout the week.

We extend our thanks to our panelists — Mayo Faulkner, Vicki Yorke-Edwards, Laura Porta, Jonas Hartmann, and SSI Fellow Batool Almarzouq — for generously sharing their time and career insights with participants.

Finally, we appreciate the contributions of those who brought creativity and fun to our social events. Jesse Krichefski and Ryan Cini prepared questions for our pub quiz, and the creative group pastagang performed live-coded music and visuals in a collaborative jam with OSW participants.

The most important people to thank are the participants themselves, who trusted us with a week of their time, and contributed not only intellectually, but also by shaping a positive and supportive atmosphere. We are greatly enriched by our interactions with them, and we hope they were too.

I’ve been giving a talk called “ConveRSE - Let’s Talk About Mental Health” as part of my SSI Fellowship. I most recently gave the talk at the Alan Turing Institute, and I thought I’d write a brief update on how it went. But also, during that talk, I used Mentimeter to ask the audience some questions, and in this blog post, I wanted to take an initial look at some of the responses to those questions. 

ConveRSE at the Alan Turing Institute

I was invited by David Beavan and Levan Bokeria to speak at the Turing as part of their Tech Talks series. I always try to attend these events in person, because I think it's important given the subject matter. Plus, I like to hang around so I can talk to people afterwards.

I arrived at the British Library early, giving me a chance to explore the building and its amazing collections, including some of Leonardo Da Vinci’s notebooks. I then made my way past an original Enigma Machine and into the Turing itself. It’s an impressive space; surprisingly light, with fancy coffee machines, well-stocked fridges and free fruit for staff and guests. It feels like it would be a nice place to work, which was only enhanced when the big screen in the entrance changed to show that there were more than a dozen Mental Health First Aiders working there!

We went into a meeting room, and I presented to around 15 people in the room and online. The talk was a variation of the one I gave at RSE Con, but it’s constantly evolving (because I’m a perfectionist with ADHD who can’t leave the flipping thing alone!). We had lots of time for Q&A, plus I chatted to a few members of the Turing REG (Research Engineering Group) before and after the talk. I also got to meet with David (as I am Vice-President of the RSE Society and he’s the President), to discuss the onboarding of new Trustees and our plans for the next twelve months.

The talk seemed to go well; everyone was friendly and welcoming, and my meeting with David meant we got a lot more done than we would have been able to over Zoom. So, a very productive day, all in all. And I haven’t even got to the data yet!

The Questions

At the end of the talk, I switched over to Mentimeter -  an interactive tool that allows the audience to use their phones or laptops to respond to questions from the presenter. 

I ask two questions during the talk:

1. What are your biggest challenges/barriers to mental health in the workplace?
2. Do you have any tips or advice for managing mental health, or any good examples of things people have done to support the morale of their teams?

The first question helps us understand the most common issues, which tells us where we should focus the efforts of the ConveRSE project. The second question is potentially more interesting, if harder to answer. I was hoping that it would result in some good tips and advice - for individuals and for leaders - that we can feed back into conversations, advice and blog posts for the project.

The Data

So, was that the case? Well, let’s take a look at the data, but first, some context.

Participation + Responses

First, some stats:

• 108 participants logged on to Mentimeter during various talks, including at RSECon and the Turing. 
• Each question received responses from around 87% of the participants.
• Participants can submit multiple responses to each question. We got 128 responses to Question 1 and 197 responses to Question 2.

Analysis

So far, we have only been able to do basic analysis on the data. The responses were free text, so the data is qualitative. To do this initial review of the data, I have taken two approaches:

1. Using Power BI, I created a Word Cloud for each question. This is essentially a count of how many times each word was used. This is how the visual featured earlier in this post was created.
2. I have attempted to categorise the submissions and amalgamate them, as described below.

Each response was assigned a number of categories. For example:

• Amalgamating different spellings (“impostor syndrome” and “imposter syndrome”)
• Combining similar advice: (lots of people mentioned “fresh air”, “nature”, “touching grass” or “get outside”).
• Separating multiple responses. For example, one response was: “Yoga, Work from home more often, Team lunch on pay day, No work on weekends", which was assigned four categories.

There is more work to be done, but this initial processing has allowed us to take a look at the most common responses to each question.

Question 1 Results

Question 1 was “What are the biggest challenges/barriers to mental health in the workplace?” The graph below shows the number of times each of the most common issues was mentioned. 

The three most reported issues were: Workload (22 responses), Context Switching (13) and Impostor Syndrome (11). These are common issues that have cropped up in various conversations over the last few months. You could argue that these are just part of everyday life for RSEs, but there must also be more that we can do to mitigate these issues, or to support people who are struggling with them.

The next two most reported issues were Workplace Culture (9) and Management/Leadership (7). This just goes to show how important leaders and line managers are, both in supporting individuals and in supporting their teams.

This data seems to support my current conclusions from my Fellowship so far:

1. Self-care is important, and we need to provide people with the information, support and tools they need to look after themselves.
2. We need to give leaders and line managers the tools they need to manage not just the projects and workload of their teams, but the morale and wellbeing too. 

Question 2 Results

Question 2 was “Do you have any tips or advice for managing mental health or any good examples of things people have done to support the morale of their teams?”. The graph below shows the number of times each suggestion was made.

The top three suggestions were Exercise (25), Socialising - both with colleagues and outside of work - (24) and Setting Boundaries (21). Touching Grass (i.e. getting out into nature) was another popular one, along with hobbies, mindfulness and making sure to take breaks and holidays.

Setting Boundaries is anything that involves establishing a clear separation between work and home, such as breaking up the day when working from home and protecting personal time. Similarly, there is “No Notifications” (8), which could mean not having work Slack or work emails on your phone, or having designated quiet times where you focus on work without interruptions (Incidentally, I have recently written a blog post about both of these things on the ConveRSE Website).

There were also a few interesting insights that came out of the data, even though they weren’t the top-scoring categories. For example, a few of the suggestions were specifically to find hobbies “that do not look like work”. I’m guilty of this; a lot of my hobbies involve sitting in the same room, at the same desk, using the same computer and staring at the same screen that I’ve just been using all day for work!

Final Thoughts

I think that giving these talks in person has been a very useful experience. The conversations I’ve had continue to inform the ConveRSE project, and the Mentimeter data has been a good source of information about common issues in the community.

I acknowledge that there is a balance to be struck here. It’s good to know what the most common problems are, as by focusing on them, we can make the biggest impact on the community as a whole. But we also don’t want to ignore the less common issues, as we don’t want to neglect or marginalise anyone. 

However, this experience has reaffirmed my belief that we make a difference by providing leaders with tools to support their teams and providing individuals with the tools they need to look after themselves.

Thanks for reading. If you’d like me to give my “Let’s Talk About Mental Health” talk at your institution, please get in touch (the SSI Fellowship will cover travel, accommodation, etc. until the end of March 2026).

Take care of yourselves!

Launched in 2021, SSI Fellow Peter Schmidt’s Code for Thought podcast has become an important space for conversations about research software and the people who make it. In a recent episode, Peter speaks with three of our 2025 SSI Fellows about their motivations, research interests, and what they hope to achieve through the SSI Fellowship Programme.

Event info:

For the first week of June 2025, I was at the ELIXIR All Hands meeting in Thessaloniki, Greece. ELIXIR is an intergovernmental European life sciences infrastructure with members from over 240 research institutes in 21 countries. All Hands is an annual event bringing together members of the ELIXIR community and partner organisations from across Europe to review ELIXIR’s achievements, ongoing activities and future plans.

This year was the 11th annual meeting - my 3rd All Hands. The event was full of opportunities to build networks and community, as well as learn about inter/national successes and challenges to anything life science infrastructure related. I was also there as a participant in the second cohort of ELEAD, ELIXIR’s leadership and diversity mentoring programme to support women’s leadership growth in ELIXIR.

Pre-All Hands:

I flew to Thessaloniki early to attend a networking dinner and peer-mentoring workshop as part of the ELEAD programme. This was the first time our ELEAD cohort met in person, along with the ELEAD programme team and our trainer, Louise Schubert. We had a lovely dinner on the Sunday evening, full of good food and positive connections with my female colleagues.

The next morning, we were all up bright and early for our workshop. Starting with an introduction to peer mentoring and how it is set up for ELEAD, we formed our peer mentoring groups, an essential part of ELEAD. Throughout the programme we meet regularly in our groups to reflect on our own professional practice and support each other through career successes and challenges. It’s a very rewarding part of ELEAD and I felt right at home with the rest of my group - being honest about things we have been finding difficult at work quickly brought us close together, and I left the workshop feeling a lot of inspiration and gratitude.

All Hands:

Day 1:

Then it was time for the main event! Which importantly started with lunch.

As always, the first session was opening remarks from the host node (Greece) followed by a keynote from Naveed Aziz, Vice President of R&I at Genome Canada, who covered infrastructure and governance similarities between EU and Canada and an interesting overview of the past 25 years of Genome Canada. 

After a coffee break, it was time for the first parallel sessions. I went to the mini-symposium on Cross-border Access to Human Genomes and Linked Data at Scale. This session covered advances in European genomic data infrastructure, including federated infrastructure and its practical barriers, and a walk through of how ELIXIR is involved with the European Cancer Mission, before ending with a panel discussion. The day ended with a very busy poster session and welcome drinks at the venue.

Day 2

The second day kicked off with 2 back to back parallel workshop sessions. I first attended the workshop on Enhancing RDM Resources led by the ELIXIR RDM community. After a brief introduction, we discussed various RDM topics, from incentives, physical data needs, and RDM training for overlooked professions.

Then I went to the workshop led by the ELIXIR Cancer Data community, Trends in Services for Cancer Research. Here I learnt a lot about cancer data (I work with musculoskeletal data but we covered a lot of relevant topics such as multi-omic data integration), as well as standards such as DOME for improving trust in AI.

There was then a 90-minute lunch & networking break - a great chance to catch up with international colleagues and have a more in-depth look at the posters when it’s less crowded. It was then time for the second plenary, Global Collaborations: Perspectives from Research Infrastructures, with representatives from Euro-BioImaging, Instruct-ERIC, and the ELIXIR Staff Exchange and Global Engagement initiatives. One set of flash talks and fascinating panel discussion later, I had a much better idea of the achievements, challenges, and opportunities that come with large international collaborations.

Another coffee break, then the final parallel session of the day - 3 mini-symposia on biodiversity data, empowering knowledge sharing, and node and people development. I skipped this session - it had been an intense 2 days so far and I needed a break if I was going to make it to the end! The evening ended with the ELIXIR-UK node dinner, unsurprisingly as we’re in Greece there was amazing food, a great chance to catch-up with UK colleagues.

Day 3

It was again a jam packed day of workshops, a plenary, and symposia. First, I went to the ELEAD workshop where we heard about other leadership initiatives for women in infrastructure in Europe and beyond, before a very interactive session mapping all initiatives we knew of and reflecting on which ideas could be useful for us to put into practice.

Then I sat in the ELIXIR & EOSC workshop, an important and exciting discussion around the future development of EOSC nodes, how they’re structured and linked with ELIXIR, and how to stay up to date on EOSC developments and strategy. I came away with more knowledge of EOSC than the year before but still a bit confused - initiatives as big as EOSC are hard to get your head around!

There was then a long lunch/networking session, where I met my ELEAD mentor for the first time. Another key part of ELEAD is being paired with a senior mentor to support your career development - it was exciting to finally meet each other and start this process. There was another plenary on ELIXIR Node Roles, Services, and Connections, an informative session from the ELIXIR Hub and several national nodes on the different node coordinator roles and how the nodes and ELIXIR hub interact and engage on various projects and services.

The final session of the day I went to was on Federated Service Delivery: Enabling Sensitive Data Computing in ELIXIR, covering the complex additional needs of sensitive data, what projects are working on this in ELIXIR, other domains we can learn from (e.g. climate data), ending with a discussion on all the above and what is needed to federate compute services in ELIXIR.

The day didn’t end there! That evening was the conference dinner at another venue in Thessaloniki. We had a nice drinks reception overlooking the sea before heading inside for a delicious meal accompanied by a fantastic display of traditional Greek dancing and music. 

Day 4

The final day had sadly arrived. Again, it kicked off with parallel workshop sessions - I went to a very engaging workshop on Data Annotation and Representation delivered by colleagues from the University of Nottingham. After a brief introduction to the workshop, we were split into two teams, debate style, to argue for or against the contentious statement: “All annotated datasets are unreliable”. We had a lot of interesting discussions in our teams before a fun debate at the end.

A quick pit-stop for coffee and then the closing plenary session. Irene Papatheodorou gave an insightful talk on her work on phenotypes at the Earlham Institute, and then we heard an overview of ELIXIR’s 2026 plans before poster prizes were awarded. The session ended with the most anticipated slide of the meeting, where is next year’s All Hands? [Drum roll] Lyon, France!

Lunch was a final chance to say goodbye to colleagues before heading back home. It was a fantastic All Hands as always, and although I was very exhausted from an intense 4 days of networking and new information, I left feeling very connected, inspired, and full of ideas. Until next year.

Slides, posters, and an event report from ELIXIR All Hands 2025 are available to all.

Thank you to the Software Sustainability Institute for funding my accommodation for this meeting.

The SSI Fellowship Programme supports passionate individuals in research and software, empowering them as ambassadors of good practice to shape the future of research software. The selection process for this year’s cohort has now ended and we’re excited to introduce the 2026 Fellows and share their plans for the Fellowship.  

For the 2026 cohort, we received 85 applications from 57 institutions, spanning 38 research areas based in 16 countries. After rigorous review – 255 assessments by 39 reviewers, mostly SSI Fellows, staff, and collaborators – we shortlisted 39 candidates.  

The shortlisted applicants participated in our Online Selection Day, featuring group discussions and event planning activities that tested collaboration, communication, and contribution. Based on these activities and initial scores, 25 wonderful new Fellows were selected to join the Fellowship Programme.

Insights from the 2026 Selection

Continued improvement of support

Following last year’s changes to improve transparency, including clearer eligibility criteria and the publication of our shortlisting and online selection day criteria, we continued to build on this momentum. We expanded our ‘Ask Me Anything’ sessions and doubled the number of Fellows available for support to applicants, increasing from 10 to 20. While it’s difficult to draw a direct link, we saw a notable rise in high-scoring applications with submissions rated 4/5 or higher increased by nearly 50% (from 20 to 31), alongside a 23% rise in total applications (from 69 to 85, a new record). Importantly, all 85 applications progressed for review this year, compared with 69 out of 75 last year.

Broadening horizons

In relation to our continued dedication to broaden our engagement, the 2026 cohort includes Fellows from six institutions that have never been represented before in the Fellowship Programme. We also welcomed applicants from fields that have historically been underrepresented in the programme, including the Creative Arts, Education, Medicine and Dentistry, Linguistics, Sociology, and most notably the Biological Sciences, from which five Fellows were selected.

Gender and career trends

While most applicants continue to be men (55%), candidates who identified as women, non-binary, or preferred not to disclose their gender had higher success rates at every stage of the selection process, making up 64% of selected Fellows, mirroring trends from last year. Early-career applicants represented 48% of selected Fellows. Under current criteria, Research Software Engineers (RSEs) are placed in the early-career category. However, we recognise that RSEs vary widely in experience. To support clearer and more accurate alignment, we plan to review how the RSE career path corresponds to our current (academic) career stages. We also see limited applications and lower success rates from Phase 4 applicants. Since we value applicants at this stage, we are reviewing our processes, criteria, and communications to clarify expectations for both applicants and reviewers.

Evolving leadership in the community

Last year’s strong participation from RSEs highlighted both the growing recognition of technical and research software roles and their increasing confidence to step into leadership positions. This year, we again saw strong representation, with 10 of the 25 selected Fellows (40%) working in RSE or similar technical roles. However, we also selected more Research-Focused Academic roles (7 Fellows, or 28%), which creates a well-balanced cohort. We would love to see even more junior and early-career researchers apply in future cycles to maintain this balance.

In addition, this year we saw an increase in applications from those in Leadership or Community Management roles, with 5 Fellows (20%) selected. This reflects the growing recognition of community-building roles within the research software ecosystem and – like their RSE colleagues – their confidence to take on leadership positions in the research software community. This also highlights how the SSI Fellowship Programme is becoming a hub of expertise for people who create, sustain, and professionalise communities of practice across the research software landscape.

The Plans of the 2026 SSI Fellows

The new Fellows bring forward a broad array of plans that highlight the broad impact of the Fellowship Programme. They are establishing diverse Communities of Practice (CoPs) and peer networks across areas including ethical and reproducible AI, green and sustainable computing, inclusive and neurodiverse research practices, creative computing, and specialised research domains such as chronobiology, high-energy physics, and taxonomic research.

Their projects combine practical training, workshops, hackathons, and community-led events to improve coding practices, build grassroots networks, and foster collaboration between research software engineers, domain specialists, and artists. Several Fellows are developing tools and resources to enhance reproducibility, sustainable computing, and open science, including lightweight computing environments, workflow templates, and AI fairness frameworks.

These initiatives extend globally, linking communities in the UK, Latin America, Asia, and Australia, while addressing inclusivity, mental health, and professional development across research software and data-science communities. By connecting training, open-source development, and community-building efforts, the 2026 cohort advances research software practice, fosters responsible AI adoption, and strengthens the foundations of open and collaborative science.

Challenges and Opportunities  

While we’re celebrating this year’s successes, we’re also reflecting on where we can improve:  

Improving diversity

Applications this year show a trend of increased ethnic diversity, with good representation across all ethnic groups. However, the data highlighted some disparities during shortlisting and selection. For example, applicants from Asian or British Asian backgrounds saw a drop from 17.7% of applications to 10.3% shortlisted, and ultimately 8% confirmed in the cohort. Applicants from Mixed or multiple ethnic groups and Other ethnic backgrounds also experienced small decreases during selection, but this is an improvement on last year. We are constantly reviewing our selection procedures to identify barriers and ensure our processes are fair, transparent, and inclusive, reflecting the diversity we aim to support.

Reaching new disciplines

While Computer Science continues to be the largest applicant group, applications from Physical Sciences and Social Sciences have slightly improved on last year, with a notable increase in selected Fellows from the Biological Sciences (+5 on a total of 24 Fellows within the entire Programme historically). Encouragingly, outreach to Arts and Humanities researchers last year has continued to strengthen representation from these disciplines in this year’s cohort. Expanding engagement with underrepresented fields such as the Creative Industries and the Social Sciences in future calls will help build a more multidisciplinary Fellowship Programme that reflects the full spectrum of research software needs.

Refining evaluation

Differences between shortlisting scores and final selections indicate areas where evaluation criteria could be clearer and more consistent. In particular, we are reviewing the processes around the Online Selection Day to make expectations clearer for both applicants and reviewers, ensuring that everyone can engage fully and confidently in the process. More broadly, we are considering how the format and criteria can be more inclusive by accounting for diverse cultural norms, communication styles, and ways of presenting oneself, so that all candidates are evaluated fairly and equitably. Finally, we also aim to put in place financial support where needed (e.g. to cover costs such as upgraded internet packages) so that all candidates can fully participate in the Online Selection Day.

Looking Ahead  

The SSI Fellowship Programme is about more than professional development. It’s about building a vibrant, supportive, and inclusive research software community. The 2026 cohort illustrates this mission, bringing together diverse backgrounds, a wide range of disciplines, and ambitious projects that advance open science, reproducible research, sustainable computing, and community-building. Their work spans AI ethics, creative computing, green computing, high-energy physics, chronobiology, and beyond, connecting researchers across the UK, Europe, Latin America, and Asia.

To our new Fellows: welcome to the SSI community! We can’t wait to see how your work takes shape and the positive change you’ll inspire.   

To everyone else: keep an eye out for updates on these exciting projects and if you’re interested in what they are doing consider getting in touch via fellows-management@software.ac.uk. 

If you’re passionate about research software, think about applying next year. Together, we can shape the future of sustainable, inclusive, and innovative research software. 

In September, I attended my sixth RSECon25. I wore many hats at the event, but I was mainly there with my SSI fellowship hat on. I had the opportunity to talk to RSE Leaders and the other attendees about my work on the ConveRSE project, as well as catching up with faces old and new. RSECon is always one of the highlights of the year for me (along with Collaborations Workshop, obviously!), and this year was no exception.

Let’s Talk About Mental Health

First, I gave a lightning talk at the RSE Leaders and Aspiring Leaders Workshop on Monday. This was a great opportunity to encourage the leaders to get involved and spread the word amongst their teams. I felt it was important to talk to them, as line managers and team leaders can have a massive impact on a person’s mental health in the workplace. I was keen for them to contribute to ConveRSE by sharing tips and advice on how to look after their teams, so that we can provide all leaders with the tools to do this effectively.

Then, on Wednesday, I got to give my full talk to the audience at the conference. I told them two stories: first, my story, about my own experiences and struggles with mental health. Then, I talked about how I came to apply for the SSI Fellowship, what I’d been up to so far, my plans for the future, and how to get involved

I don’t like to think about how many people were towering over me in that colossal amphitheatre of a lecture hall. It’s difficult being an anxious person and having to talk to a room full of people about your anxiety! However, the talk included an interactive element, using Mentimeter, and there were 100 people who contributed, both in the room and online. Thank you to everyone who contributed. I plan to do a separate blog post to discuss the data I collected at a later date.

The talk seemed to go well. I was grateful to have such a large audience, given that there were five tracks of incredible talks, workshops and other things going on. I got a lot of good feedback and had a lot of interesting conversations after the talk, as well as during my time on the RSE Society and SSI stands. I gave out a lot of stickers and leaflets too!

The Society will be posting recordings of all of the talks on their YouTube Channel in the coming months, so if you weren’t at RSECon or missed the talk, you will be able to catch up. I would also love to continue the conversation, so please get in touch if you would like me to deliver a version of this talk at your institution.

The rest of the event

I didn’t get to go to a huge number of other talks. I also had to wear my RSE Society Trustee hat, and my duties included addressing the AGM, overseeing this year’s trustee elections and announcing RSECon26, and its co-location with the first International Research Software Conference. I also decided to take my own advice and stay hydrated and take plenty of breaks, which I’m usually pretty bad at at conferences!

I was also delighted to be one of four official Mental Health First Aiders at the event. I know a few people needed to make use of our services, so I’m glad the conference organisers invited us to be part of it (and I’m grateful to the SSI for sponsoring my training as part of my fellowship).

I enjoyed the keynotes from Amanda Brock, Simon Hettrick and Tania Allard. Another highlight was one of the other talks in my session: “Let's stop pretending to be Unicorns” by Marion Weinzierl. It was an interesting discussion about how the traditional role of plug-and-play, generalist RSEs who are expected to do everything might not always be the best solution for RSEs or the researchers we collaborate with, including some discussion of how trying to be a unicorn affects our mental health.

Finally, I was delighted to finally get to watch (and meet) Matt ‘StandupMaths’ Parker, who had to cancel a previous appearance at the conference due to Covid. A good laugh was just what we needed at the end of a long day of conferencing!

Final Thoughts

This may have been the most nervous I’ve been giving a talk at a conference, but as always, the research software community were kind, welcoming and supportive. I got to have a lot of interesting conversations, some of which have spawned new ideas for the ConveRSE project, plus I had a few offers for contributions to the website, including both code and blog posts.

My goal is to continue the conversation around mental health in this community, and I don’t think I could have asked for a better opportunity to try and do that.

At  RSECon25 in Warwick, the Cloud Native SIG team ran their opening event, a workshop for people looking to get started with Kubernetes. It was a success, with a packed out room and a separate pod of conference attendees following the workshop online. We certainly managed to scale our workshop appropriately! We received a lot of positive feedback and exciting contributions from participants. If you did not manage to attend or are looking for further reading, you can view the tutorial in its entirety. A big thanks to Alex Lubbock for the Kubechaos App and Lewis Sampson and Piper Fowler Wright for the content and teaching.

The event was enjoyed by 80 people, and included material on Kubernetes architecture, Helm and practical examples for deploying your applications robustly and scalably. There was lots of great developer energy and support in the room and we fixed all manner of technical bugs and got some excellent contributions both to the course material and to our Kubechaos App, which we are currently reviewing. There are some really creative Javascript developers in the RSE community.

We had lots of positive feedback highlighting the workshop’s impact in the community. Wahab Kawafi from the Bristol Centre for Supercomputing shared this endorsement, "with cloud native workflows gaining popularity with researchers, it's great to finally have a resource to upskill RSEs in using Kubernetes and Helm". To continue this support, we have made the course open source and plan to do further events exploring other areas of Kubernetes. 

If you would like to hear more about the Cloud Native SIG please join our mailing list. We are hoping to release a website very soon and will keep you posted with details. Do you have your own adventures using Cloud Native technology that you would like to share? We would very much like to hear from you. Please email laura.shemilt@rfi.ac.uk if you would like to provide a short blogpost on your experience.