JGI support – Jean Golding Institute News

Meet the Ask-JGI team – Adrianna, Fahd, Yujie & Huw

Posted on 17 February 202517 February 2025 by kerry.turcsi

The new Ask-JGI helpdesk cohort started in September 2024 and have been busy answering queries from researchers across the university! We introduced half of the team in our January blog. Meet the other half of the team below:

Adrianna Jezierska (she/her) – Ask-JGI PhD Student

Adrianna Jezierska, PhD candidate in in the School of Business

I’m a PhD student at the University of Bristol Business School. My project focuses on social media influencers and their vegan content on YouTube. Using language derived from video transcripts, I analyse to what extent they legitimise veganism so that it becomes popular and desirable in society. Whilst most organisation and management scholars have developed theories based on qualitative data, resulting in small datasets and case study approaches, in my work, I highlight the role of computational social sciences and big data in helping social scientists answer their research questions.

Coming from a social science background, I was initially hesitant about joining the Ask-JGI team. However, this decision has turned out to be the most rewarding and challenging experience. Being part of the team is a continuous learning journey. The questions we receive span various disciplines, often pushing us out of our comfort zones. The most exciting part of the job is the opportunity to communicate with other researchers and receive their positive feedback. On the other hand, we constantly collaborate with other team members and learn from each other, which makes it a very supportive environment. I’m pleased to see more queries from social scientists and humanities researchers. The growing popularity of computational approaches and the shift towards interdisciplinary research is a trend that I find inspiring and exciting

Fahd Abdelazim (he/him) – Ask-JGI PhD Student

Fahd Abdelazim, PhD student on the Interactive AI CDT in the School of Computer Science

I am a PhD student in the Interactive Artificial Intelligence CDT, specializing in model understanding for Vision-Language models. My research focuses on introducing improvements to Vision-Language models that allow for better linking of specific ideas or attributes to physical items, in order to help models recognize and understand the properties of objects in images.

I first heard of the Ask-JGI team through fellow PhD students, and it was recommended to me as a way to apply data science skills to real-world applications. Joining the Ask-JGI helpdesk has been a unique experience where I’ve been able to delve into various domains and learn about topics that I would otherwise not have had the chance to learn about. The team truly values cross-functional collaboration and encourages tackling new challenges and learning on the job.

Working at Ask JGI is incredibly rewarding. I enjoy the diversity of challenges presented by each query which gives me the chance to improve as a data scientist and gain a better understanding of how data science can help improve academic research. I really enjoy the collaborative spirit within the team. The Ask-JGI team are from many different disciplines and interacting with them allows for interesting exchanges of ideas and problem-solving approaches. This allows me to grow not just as a data scientist but as a researcher as well.

Yujie Dai (she/her) – Ask-JGI PhD Student

Yujie Dai, PhD student in the Digital Health and Care CDT

I am a PhD student in the Digital Health and Care CDT, specializing in population health data science. My research focuses on leveraging large-scale real-world health data to address critical challenges in infectious diseases. Specifically, I utilize explainable AI (XAI) techniques to characterize and diagnose diseases, aiming to bridge the gap between data science and public health.

My journey with Ask-JGI began with a recommendation from a friend who was previously part of the team. They spoke highly of the collaborative and dynamic environment, and I was intrigued by the opportunity to apply my skills in real-world research settings. Joining Ask-JGI is an extension of my academic and research pursuits. I was drawn to the idea of supporting researchers across diverse disciplines, helping them navigate technical challenges in their projects, and learning from their different perspectives. The chance to engage with cutting-edge problems and contribute to solutions beyond the scope of my own research was exciting.

There’s so much to love about being part of Ask JGI. I love the variety of work. Each question I encounter presents a new challenge, whether it’s developing a data analysis pipeline, troubleshooting code, or brainstorming creative solutions for a computational problem. The variety keeps me constantly learning and growing as a data scientist. I also love the collaborative atmosphere. Working closely with researchers from different fields gives me diverse ways of thinking and problem-solving. It’s an opportunity to not only apply my skills but also to know more about the scientific community.

Huw Day (he/him) – Ask-JGI Lead

Huw Day, JGI Data Scientist

I am a JGI Data Scientist with a background in mathematics, working on a variety of data science projects with researchers across the university using a variety of data science methodologies and techniques. I also help run the Data Ethics Club.

As Ask-JGI Lead, I am responsible for recruiting, training and the general managing of the Ask-JGI team. They’re a fantastic group and I consider myself really lucky to be able to work with them. I support some of the general queries and I’m also responsible for talking with researchers interested in costing out data science support in grant applications.

To me, the Ask-JGI helpdesk is based on the idea that any researcher who wants to do data science should be empowered to do so. Whilst we often do the data science for people, I think the most rewarding outputs from our helpdesk is when we empower researchers to do data science themselves, guiding and validating their work. It’s also a wonderful opportunity for myself and the rest of the helpdesk to learn about research across the university.

All University of Bristol researchers (including PhDs) are entitled to a day of free data science support from the Ask-JGI helpdesk. Just email ask-jgi@bristol.ac.uk with your query and one of our team will get back to you to see how we can support you.

If you’re a PhD student interested in joining the Ask-JGI team, we will do recruiting for the next academic year in summer of 2025 so keep an eye on the JGI mailing list for when we have our recruiting call. We recruit a new cohort every year but do not accept speculative applications outside of the recruiting call.

Meet the Research Data Advocate team

Posted on 11 February 202512 February 2025 by kerry.turcsi

We are delighted to announce a new pilot training scheme led by our newly-appointed JGI Research Data Science Advocates. This is a new way to take part in training in a low-stress, collaborative and supportive environment, and at the same time form a community of data scientists in your area.

The pilot will run JGI training events over a whole week in Schools, supported by a local Data Science Advocate. They will run sessions to support a cohort to undertake the training together, over the course of a week. The formal training takes only around 2-3 hours to complete, but it is anticipated that this format will allow deeper learning and more useful application to research.

To take part in the pilot (which is aimed at relatively inexperienced coders within a discipline), please email to jgi-training@bristol.ac.uk. If your school doesn’t have a volunteer, you would be welcomed at a research-adjacent community. Bios for our Advocates are below and even if you don’t need this particular training, they would love to include you in an ongoing data science community, so please get in touch.

Ruolin Wu

I am a PhD student of paleobiology diving into the mysteries of evolutionary history. Armed with code, fossils, and molecular data, I craft stories about topological and temporal pattern of animals and plants. Outside of academia, I like climbing, handcrafts, succulents and ferns of any kind.

Zhiyuan Xu

I am a 1st year PhD student focusing on data science and artificial intelligence, with a particular focus on large language models and their applications. My background includes experience in machine learning, data-driven research, and interdisciplinary collaboration to address complex problems.

Bryony Clifton

I’m a PhD student in Biochemistry, studying the molecular details underpinning neurotransmission. My project focuses on identifying the biological role for an uncharacterised intramembrane protease found in the human brain. During my PhD, I have become aware of the importance of developing tools to present complex datasets in a clear and informative way. I am excited to begin my role with the JGI where I can support others to build these skills too.

Catherine Upex

I’m Catherine and I’m a first year PhD student based in the medical school. I’m using data science and AI to understand the shape and movement patterns of the heart over different disease states. I’m also currently working on a mini-project using AI protein folding tools, like AlphaFold, and computer simulations to uncover interactions between synthetic cannabinoids and the hERG potassium channel and its relation to arrythmia risk.

Kaan Deniz

Aerospace Engineer who has intensive industrial experience in numerical modelling with a MSc degree from the University of Bristol/ Aerospace Engineering. Current PhD student in Aerospace Engineering at the University of Bristol. Research focus is numerical modelling of composite manufacturing processes.

Boy Li

I study how to synergize domain-specific knowledge with data-driven deep learning models to extract information from remote sensing imagery.

Vaishnudebi Dutta

I am an Engineering Mathematics PhD student working on model and data-driven design of combination therapies for non-small cell lung cancer. Beyond my research, I serve as the School of Engineering Mathematics and Technology (SEMT) PhD Student Representative, advocating for and supporting the academic community. I also hold a key position as the PhD Representative for the Bristol Cancer Research Network where I get the opportunity to share research updates to Clinicians, and others in the network. Additionally, I manage the network’s official X (formerly Twitter) presence, helping to disseminate research developments and maintain engagement with the broader scientific community.

Zhengzhe Peng

I am a PhD student with a diverse background in computer science, business, and over a year of IT work experience. My research applies advanced data science methods, with a focus on AI, to explore real-world challenges. I am dedicated to expanding my knowledge in these fields and eager to help others who are new to data science, working together to advance and explore new possibilities in this ever-evolving domain.

Winfred Gatua

Winfred Gatua is a PhD Fellow at the University of Bristol, specializing in Molecular Genetics and Life Course Epidemiology. Her research focuses on the triangulation of evidence between Mendelian randomization and randomized controlled trials for complex diseases. She holds an MSc in Bioinformatics, a Postgraduate Diploma in Health Research Methods, and a BSc in Biomedical Science and Technology. Transitioning from wet lab biomedical sciences to dry lab bioinformatics, Winfred is a self-taught coder passionate about open science, automation, and reproducible research in genetics. Beyond research, Winfred is dedicated to capacity building, particularly in increasing computational and data literacy among non-computer science researchers. Since 2021, she has been a volunteer instructor with The Carpentries, securing funding, hosting and instructing carpentries lessons that equip researchers with essential skills in data analysis, open science, reproducible research and best practices in scientific computing in different institutions across the globe.

PhD Connect Conference

Posted on 10 December 202411 December 2024 by kerry.turcsi

Our Turing Liaison team recently funded a number of PhD students to go to the 2024 Alan Turing PhD Connect Conference. This is one of the range of approaches we are taking to bridging the gap between the Turing’s goals and the University’s research and academics who reflect these goals.

Attendees sat around circular tables with sheets of paper and pens on the table — *Attendees at a PhD Connect conference. Photo provided by Jingrong Bai*.

Supporting PhD students to make connections and discover new collaborations through the Turing will hugely benefit students and the wider data science and AI community, and is an important part of our objective. Below are some statements from the students we funded about their experience at the conference.

Damien Wang

I am Damien, a first-year PhD student from University of Bristol and SWDTP who specializing in psychology and artificial intelligence. The past two days at PhD Connect 2024 have been incredibly fulfilling. I had the opportunity to explore a wide range of PhD projects in AI and data science, engaging in discussions with other attendees and collaboratively tackling problems by leveraging our diverse backgrounds.

Conversations with peers and insights from the panel discussions were truly enlightening. I was also fortunate to represent my group during the Mini-DSG session and deliver my own poster presentation. These experiences have boosted my confidence and skills in presenting, and I’m grateful for the valuable feedback I received on my research.

This two-day journey has inspired me to push forward with even greater motivation. A heartfelt thanks to the Alan Turing Institute and everyone I met along the way!

Ming Chen

The PhD Connect 2024 conference was an incredible opportunity to engage with peers, learn from industry experts, and explore real-world applications of data science and AI. My research interests include learning sciences and emerging technologies in language learning. I would say that one of the highlights for me was participating in group research discussions, which broadened my understanding of AI’s role in addressing societal challenges.

I also appreciated the networking opportunities and the chance to discuss my research with fellow attendees and professionals from diverse sectors. Another interesting part of the conference is the Research Karaoke, which is a great experience for people to have fun and practise doing presentations.

Jizhao Niu

I am grateful to The Jean Golding Institute for funding my attendance at the conference. It was a fantastic opportunity to meet many PhD students from Bristol and beyond, engaging in discussions on health sciences-related projects.

A highlight for me was the training session on how to pitch research effectively, which provided valuable insights and practical skills. We worked as a team to sell an item to other groups, which was both enjoyable and educational.

I learned the importance of tailoring research presentations to audiences with diverse backgrounds — a skill I look forward to applying in the future!

Jingrong Bai

During the conference, we got insightful points on AI-human by Piotr Mirowski from DeepMind. Then, we interacted with the group work and presented karaoke, which was good for us to connect with other PhD students across the UK, also, learned how to prepare a good presentation by Beatriz Costa Gomes. Last but not the least, we shared our research ideas through the poster session. All in all, it is a valuable experience for me to know the AI field and meet all of the awesome people, really appreciate all of the speakers, organizers and students.

Jingrong Bai (left) standing in front of a poster with two other individuals discussing the posters on display — *Jingrong Bai (second on the left) with other PhD students at a networking sessio*n.

Zia Saylor

Zia Taylor (left), Kerstin Nothnagel (centre) and Michael Rumbelow (right) at PhD Connect — *Zia Saylor (left), Kerstin Nothnagel (centre) and Michael Rumbelow (right) at PhD Connect*.

Perhaps my favorite session was the one on day 2 morning of the conference when we discussed the principles of a good academic presentation. Focusing on basics like practice, maintaining relevancy to the audience, and ensuring that materials were packaged in an alluring way were key methods discussed. Looking at the AI aspect of our learning opportunities, much of the conference consisted of hands-on opportunities to engage with the materials, from designing a workflow that would integrate AI into academia without infringing on the rights and words of academics to developing a mechanism to integrate data on building pricing into an AI cost estimation algorithm that could be made. This enabled us as students to learn more about AI in its many forms and potential for interdisciplinary applications.

Jay Liu

It has been a wonderful journey for me to attending the 2024 Alan Turing AI PhD Conference at Horizon Leeds. It is my first time travelling to Leeds, a fantastic city with fancy malls and restaurants. I am grateful for the great opportunity and generous funding for the program!

I am a PhD student in Finance at the University of Bristol Business School, focusing on understanding the effects of AI and algorithmic decision making in the financial markets. I believe the conference can further improve my understanding on AI and the application of AI on interdisciplinary research!

Jay Liu standing in front of a digital screen showing a slide titled 'Welcome to the PhD Connect' — *Jay Liu standing in front of a digital screen at PhD Connect*.

Alan Turing Institute tote bag (right) featuring Alan Turing's face on it and Jay Liu's name badge (left) for PhD Connect — *Jay Liu standing in front of a digital screen at PhD Connect*.

Zhengzhe Peng

Numerous speakers standing at the front of the room in front of a slideshow projected on a wall — *Session from PhD connect with multiple speakers*.

Attending the PhD Connect Conference organized by the Alan Turing Institute was an enriching experience. I particularly appreciated the diverse perspectives shared during interdisciplinary discussions on data science applications. The keynote sessions inspired new ideas for integrating AI into my research, while the networking opportunities allowed me to connect with peers tackling similar challenges. I gained valuable insights into emerging methodologies and practical approaches that will enhance my PhD work.

Boyang Yu

This conference let me engage with the Mini-data group to explore data science applications in real-world challenges, which is what I’m doing as a PhD. I enhanced my presentation skills and learned to communicate complex ideas to a broader audience, inspired by a standout example from the presenter (Dr Beatriz Costa Gomes). I saw some very nice posters and great to have a picture with one of my most favourite poster (and its owner).

Female speaker on stage behind a lectern with a projected slide behind them showing 'Today's agenda' with timings and session titles — *Damien Wang (left) and Boyang Yu (right) at a poster session at PhD Connect*.

Ding Li

Attending the 2024 Turing Phd connect conference is such an unforgettable experience. I have met a bunch of bioinformatics students from various universities and institutions sharing their research with AI and Machine Learning. The poster and presentation session left me with impression on how research from other fields could help with my own PhD project. During the session, I discussed with Mr Muizz who is also from University of Bristol, but another school of Engineering Mathematics, and heard about how he applied AI on topology of insects’ wings in traditional species classification and phylogeny. It would never happen if there were no such an opportunity.

Ding Li standing in front of a poster with two other male individuals conversing about the poster — *Ding Li (Left) listening to talks given by data scientist Dr Piotr Mirowskifrom Google Deepmind*.

Kerstin Nothnagel

Attending the Alan Turing Institute PhD Connect Conference was an incredible experience. Highlights included Dr Piotr Mirowski’s inspiring keynote on human-machine collaboration and the ‘Mini Data Study Group,’ where we tackled real-world challenges like ICU surge prediction and cancer forecasting.

This event was a perfect prelude to my upcoming ATI funded UK-Italy Trustworthy AI Visiting Researcher Programme in Milan, where I’ll collaborate with global researchers to explore ‘Global AI Policies and Regulations and Their Impact on Healthcare.’ The project is reinforced by the importance of unifying AI policies to ensure technology benefits everyone equally, closing economic gaps rather than widening them.

Foodscapes: visualizing dietary practices on the Roman frontiers

Posted on 26 September 202426 September 2024 by kerry.turcsi

JGI Seed Corn Funding Project Blog 2023/24: Lucy Cramp, Simon Hammann & Martin Pitts

*Table laid out with Roman pottery from Vindolanda ready for sampling for organic residue analysis as part of our ‘Roman Melting Pots’ AHRC-DFG funded project*

The extraction and molecular analysis of ancient food residues from pottery enable us to reconstruct the actual uses of vessels in the past. This means we can start to build up pictures of dietary patterns in the past, including foodways at culturally diverse communities such as the Roman frontiers. However, there remains a challenge in how we can interpret these complex residues, and both visualise and interrogate these datasets to explore use of resources in the past.

Nowadays, it is commonplace to extract organic residues from many tens, if not hundreds, of potsherds; within each residue, and especially using cutting-edge high-resolution mass spectrometric (HRMS) techniques, there might be several hundred compounds present, including some at very low abundance. Using an existing dataset of gas chromatography-high resolution mass spectrometric data from the Roman fort and associated settlement at Vindolanda, this project aimed to explore methods through which these dietary information could be spatially analysed across an archaeological site, with a view to developing methods that could be applied on a range of scales, from intra-site through to regional and even global. It was hoped that it would be possible to display the presence of different compounds in potsherds recovered from different parts of a site that are diagnostic of particular foodstuffs, in order to spatially analyse the distribution of particular resources within and beyond sites.

*A fragment from a Roman jar that was sampled from Vindolanda for organic residue analysis as part of our ‘Roman Melting Pots’ AHRC-DFG funded project*

The project started by processing a pilot dataset of GC-HRMS data from the site of Vindolanda, following a previously-published workflow (Korf et al. 2020). These pottery sherds came from different locations at the fort, occupied by peoples of different origins and social standings. This included the praetorium (commanding officer’s house), schola (‘officers’ mess’), infantry barracks (occupied by Tungrians, soldiers from modern-day Belgium and Netherlands), and the non-military ‘vicus’ outside of the fort walls likely occupied by locals, traders and families. Complex data, often containing several hundred compounds per residue were re-integrated using open-source mass spectrometry data processing software MZ Mine, supported by our collaborator from MZ IO gmbh, Dr Ansgar Korf. This produced a ‘feature list’ of compounds and their intensities across the sample dataset. This feature list was then presented to Emilio Romero, a PhD student in Translational Health Sciences, who worked as part of the Ask-JGI helpdesk to support academic researchers on projects such as these. Emilio developed data matrices and performed statistical analyses to identify significant compounds of interest that were driving differences between the composition of organic residues from different parts of the settlement. This revealed, for example, that biomarkers of plant origin appear to be more strongly associated with pottery recovered from inside the fort compared with the vicus outside the fort walls. He was then able to start exploring ways to spatially visualize these data, with input from Léo Gorman, a data scientist from the JGI, and Levi Wolf from the School of Geographical Sciences. Emilio says:

‘Over the past year, my experience helping with the Ask-JGI service has been truly rewarding. I was very excited to apply as I wanted to gain more exposure to the world of research in Bristol, meet different researchers and explore with them different ways of working and approaching data.

One of the most challenging projects was working with chemometric concentrations of different chemical compound residues extracted from vessels used in ancient human settlements. This challenge allowed me to engage in dialogue with specialists in the field and work in a multidisciplinary way in developing data matrices, extracting coordinates and creating maps in R. The most rewarding part was being able to use a colour scale to represent the variation in concentration of specific compounds in settlements through the development of a Shiny application in R. It was certainly an invaluable experience and a technique I had never had the opportunity to practice before.’

This work is still in progress, but we have planned a final workshop that will take place in mid-November. Joining us will be our project partners from the Vindolanda Trust, as well as colleagues from across the Roman Melting Pots project, the JGI and the University of Bristol. A funding application to develop this exploratory spatial analysis has been submitted to the AHRC.

Contact details and links

You can find out more about our AHRC-DFG funded project ‘Roman Melting Projects’ and news from this season’s excavations at Vindolanda and its sister site, Magna.

A real-time map-based traffic and air-quality dashboard for Bristol

Posted on 24 September 202426 September 2024 by kerry.turcsi

JGI Seed Corn Funding Project Blog 2023/24: James Matthews

Example screenshot of the Bristol Air Quality and Traffic (AQT) Dashboard with Key — *Example of the dashboard in use.*

A reduction in urban air quality is known to be a detrimental to health, affecting many conditions including cardiorespiratory health. Sources of poor air quality in urban areas include industry, traffic and domestic wood burning. Air quality can be tracked by many government, university and citizen held pollution sensors. Bristol has implemented a clean air zone, but non-traffic related sources, such as domestic wood burning, are not affected.

The project came about through the initiative of Christina Biggs who approached academics in the school of Engineering Mathematics and Technology (Nikolai Bode) and the School of Chemistry (James Matthews and Anwar Khan) with a vision for an easy to use data dashboard that could empower citizens by drawing data from citizen science, university and council air quality and traffic sensors in order to better understand the causes of poor air quality in their area. The aims were to (1) work with community groups to inform the dashboard design (2) create an online dashboard bringing together air quality and traffic data (3) use council air quality sensors to enable comparison with citizen science sensors for validation and (4) to use this to identify likely sources of poor air quality.

An online dashboard was created using R with Shiny and Leaflet, collecting data using API code, and tested offline. The latest version of the dashboard has been named the Bristol Air Quality and Traffic (AQT) dashboard. The dashboard allows PM_2.5 data and traffic numbers to be investigated in specific places and plotted as a time series. We are able to compare citizen sensor data to council and government data, and we can compare to known safety limits.

The dashboard collates traffic data from several sources including Telraam traffic report and Vivacity traffic data which provide information on car numbers from local sensors; and PM_2.5 data from different sources including Defra air quality stations and SensorCommunity (previously named as Luftdaten) citizen air quality stations. Clicking onto a data point provides the previous 24 hour time series of measurements. For example, in the screenshots below, one Telraam sensor shows a clear PM2.5 peak during the morning rush hour of 26^th June 2024 (a) which is likely related to traffic, while the second shows a higher PM2.5 peak in the evening (b) which could be related to domestic field burning, such as an outdoor barbecue. A nearby traffic sensor shows that the morning peak and smaller afternoon peak do agree with traffic numbers (c), but the evening peak might be unrelated. Data can be selected from historic data sets and is available to download for future interrogation.

Example of data output from the dashboard showing PM2.5 midnight to midnight on 26/06/2024 — *Figure (a) Example of data output from the dashboard showing PM_2.5*

*Figure (c) Example of data output from the dashboard showing traffic measured using local Bristol sensors*

It is a hope that these snapshots might provide an intuitive way for communities to understand the air quality in their location. Throughout the project, the project team held regular meetings with Stuart Phelps from Baggator, a community group based in Easton, Bristol, so that community needs were put to the forefront of the dashboard design.

We are currently planning a demonstration event with local stakeholders to allow them to interrogate the data and provide feedback that can be used to add explanatory text to the dashboard and enable easy and intuitive analysis of the data. We will then engage with academic communities to consider how to use the data on the dashboard to answer deeper scientific questions.

Contact details and links

Details of the dashboard can be found at the link below, and further questions can be sent to James Matthews at j.c.matthews@bristol.ac.uk

https://github.com/christinabiggs/Bristol-AQT-Dashboard/tree/main