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AI4RSE Workshop Program

The workshop will take place on Wednesday, 3 December 2025, at the Wageningen Campus (Leeuwenborch, room B063).
It will bring together researchers, engineers, PhD candidates, and IT professionals – anyone developing or maintaining research-related code, scripts, or models – to explore the role of Artificial Intelligence in Research Software Engineering.
Topics include:
  • AI tools for code development, testing, and maintenance
  • Reproducibility and sustainability in research software
  • Project experiences and use cases
Practical details
  • Date: Wednesday, 3 December 2025
  • Time: 09:00 – 16:00
  • Location: Wageningen Campus, Leeuwenborch (Room B063)
  • Audience: Researchers, engineers, PhD candidates, and IT professionals
Full-day program AI4RSE Quadrant FAIR & Quality Sustainability & Green AI Hands-on sessions
Participant Requirements for Hands-on Tracks (Afternoon)

To actively participate in the hands-on practice sessions in the afternoon (Track 2 and Track 3), please make sure you bring your own laptop and meet the following requirements:

Track 2 – Using AI4RSE Tools

  • A laptop
  • A modern web browser (e.g. Chrome, Firefox, Edge, or Safari)

Track 3 – Vibe Coding

  • A laptop with a modern web browser
  • A Google account (required to log into Google Colab)

Keynote Speakers – Morning Session

Confirmed keynote speakers for the morning programme.

Bedir Tekinerdogan
Prof. Bedir Tekinerdogan
Chair, Information Technology Group (WUR)
Beyond Automation: How AI is Transforming Research Software Engineering
Slot: 09:15 – 09:45
Carlos Martínez-Ortiz
Dr. Carlos Martínez-Ortiz
Community Manager, Netherlands eScience Center
eScience View on AI & RSE
Slot: 09:45 – 10:15
Bastiaan Boom
Dr. Bastiaan Boom
Lead ActiveAI Group, OnePlanet Research Center (imec)
Challenges and Opportunities in Creating a Digital Orchard
Slot: 10:30 – 11:00
Zhiming Zhao
Dr. Zhiming Zhao
Associate Professor, University of Amsterdam
Enhancing Research Software Quality in a Virtual Research Environment
Slot: 11:00 – 11:30
Bas van der Velden
dr.ir. Bas van der Velden
Head of Data Science & AI, Wageningen Food Safety Research
AI for Food Safety
Slot: 11:30 – 12:00
Beyond Automation: How AI is Transforming Research Software Engineering
Bedir Tekinerdogan
Prof. Bedir Tekinerdogan
Chair, Information Technology Group, Wageningen University & Research
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About the talk

Software engineering has evolved over decades into a well-defined discipline with established practices for reliability, testing, design and maintenance, and it continues to improve as systems grow in scale and complexity. Research or science software engineering builds on these foundations but operates in a context where requirements shift with new discoveries, where code often embodies scientific models, and where correctness is tightly coupled to experiment and interpretation. RSE adds further challenges to the complexities of SE: code must adapt as science advances, experiments must be reproducible, data workflows can be immense, and performance and sustainability matter as much as correctness.

AI is now disruptive across many domains, and it is reshaping software engineering itself by changing how we write, test, optimise and reason about code. In this keynote we synthesize these trends through a clear quadrant framework comparing SE and RSE with their AI-supported counterparts, illustrating how AI assists development tasks, accelerates research pipelines, supports documentation and testing, and even helps generate scientific insight. Attendees will leave with a structured understanding of how AI is transforming research software engineering, what skills and practices are becoming more important, and how to actively shape a future where human expertise and AI capability work together.

Bio

Professor Tekinerdogan is a computer scientist with over 25 years of experience in software/systems engineering and information technology. He earned both his MSc (1994) and PhD (2000) in Computer Science from the University of Twente, The Netherlands.

He has held academic positions at the University of Twente and Bilkent University, where he founded and led the Bilkent Software Engineering Group. He is currently a full professor and chair of the Information Technology group at Wageningen University. He has authored more than 400 peer-reviewed publications, edited multiple books, and led numerous national and international research and consultancy projects in domains such as consumer electronics, enterprise systems, automotive, critical infrastructures, cyber-physical systems, satellite systems, energy systems, precision farming, and more.

His expertise spans software and systems architecture, software product line engineering, cyber-physical systems, model-driven development, aspect-oriented software engineering, global software development, data science, and AI. He has extensive experience as an educator and industrial trainer, and has supervised many MSc and PhD students.

eScience View on AI & RSE
Carlos Martínez-Ortiz
Dr. Carlos Martínez-Ortiz
Community Manager, Netherlands eScience Center
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About the talk

AI is changing every aspect of society. But change itself is not new: transformative technological shifts occur with increasing frequency. What matters is how we adapt to these developments and learn to make the most of them.

In this talk, Carlos shares experiences from the Netherlands eScience Center on using AI in research software engineering. He discusses concrete examples, practical tips to follow, and common pitfalls to avoid when integrating AI into research workflows.

Bio

Carlos Martínez-Ortiz is a community manager at the Netherlands eScience Center. He has a background in computer science and is involved in various research software engineering initiatives. Through his work, he supports research communities in adopting best practices in software development, reproducibility, and the use of advanced digital technologies such as AI.

Challenges and Opportunities in Creating a Digital Orchard
Bastiaan Boom
Dr. Bastiaan Boom
Principal Member of Technical Staff, Lead of ActiveAI Group, OnePlanet Research Center (imec)
View LinkedIn profile
About the talk

Real-world environments are dynamic: weather, lighting, terrain, and obstacles constantly change, making structural measurement difficult. Agriculture adds further complexity, such as seasonal changes, crop stages, and occlusions. In fruit orchards, key processes such as pruning, root pruning, flower thinning, and fruitlet thinning are vital for healthy tree growth and stable yields, but are currently not data-driven and rely heavily on experience and agronomic expertise.

To address this, imec has developed multi-sensor mapping technology that enables efficient, high-resolution 3D scanning of entire trees. Deep learning applied to 3D point clouds and hyperspectral images can systematically estimate parameters such as fruit-bearing capacity, flower count, shoot number, and disease pressure. The next challenge is integrating these parameters into digital twin technology to guide processes like automated spraying and robotic pruning.

OnePlanet Research Center envisions that advances in 3D sensor fusion, AI, and digital twinning will help overcome the complexities of agricultural environments by supporting systematic orchard research and intelligent farm management for the future.

Bio

Dr. Bastiaan Boom is Principal Member of Technical Staff and Lead of the ActiveAI group at OnePlanet Research Center. He earned his PhD from the University of Twente (2010) and completed a four-year postdoc at the University of Edinburgh (Fish4Knowledge project).

After seven years in industry at Cyclomedia, where he led a team in computer vision and point cloud recognition, he now heads the ActiveAI team of nine researchers supporting imec with AI solutions. Bastiaan is project lead for Autonomous Pruning & Digital Orchard, coordinating National Growth Fund initiatives (NextGen Hightech Handsfree Orchards) and EU projects (AIGreenBots) on sensing, AI, robotics, and VR in orchards. He has authored multiple journal and conference papers, including publications at CVPR, and holds several patents.

Enhancing Research Software Quality in a Virtual Research Environment
Zhiming Zhao
Dr. Zhiming Zhao
Associate Professor, Chair of Multiscale Networked Systems (MNS), University of Amsterdam
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About the talk

Modern scientific research relies heavily on software and information technologies for data processing, analysis, and experimental automation. Research software is not merely a supporting tool; it is a core part of research output, essential for reproducibility and open science. Yet, reusability is often hampered by deficiencies in quality and documentation.

Several research software quality models have been proposed in different communities, but adapting them to specific domains can be time-consuming and require significant training effort. In this talk, Zhiming introduces the Research Software Quality toolkit (RSQKit) being developed in the EU EVERSE project. He demonstrates its application in a Virtual Research Environment (VRE) to improve software quality across multiple levels: the core platform, domain-specific virtual labs, and Jupyter notebooks, developed in collaboration with EU ENVRI-HUB Next and LifeWatch.

Bio

Dr. Zhiming Zhao is an Associate Professor and Chair of the Multiscale Networked Systems (MNS) research group at the Informatics Institute of the University of Amsterdam. He leads the technical development of the Virtual Lab & Innovation Center (VLIC) within the European Research Infrastructure LifeWatch.

His research focuses on programming and control models for quality-critical systems on programmable infrastructures, including clouds, edges, and software-defined networks. Supported by various EU and Dutch projects, his team develops digital twin solutions, virtual research environments, and cloud automation tools addressing data and computational challenges in industrial innovation and big data infrastructures. He is a Senior Member of the IEEE and Managing Editor of the Journal of Cloud Computing.

AI for Food Safety
Bas van der Velden
dr.ir. Bas van der Velden
Head of Data Science & AI, Wageningen Food Safety Research
View personal page
About the talk

In this talk, Bas van der Velden elaborates on the use of Artificial Intelligence (AI) for food safety. He discusses trends in food safety research and presents several use cases in which deep learning is used to keep our food system safe, working with chemical, biological, and image-based data.

Bio

dr.ir. Bas van der Velden is the Head of Data Science & AI at Wageningen Food Safety Research, where he leads a diverse, international team of researchers working on AI for chemical, biological, and image-based data. His team leads multiple work packages in European projects, and Bas is a member of the innovation subgroup of the European Food Safety Authority (EFSA) Advisory Group on Data.

Bas holds a PhD in Medical Image Analysis from Utrecht University. With over a decade of experience in deep learning and explainable AI, he helps translate complex models into actionable insights for researchers, policymakers, and industry partners.

Workshop Program

Below is the schedule for the AI4RSE workshop.

Morning Session

All morning sessions take place in Room B063 (Leeuwenborch).

Time Session / Talk Speaker / Facilitators Notes
08:30 – 09:00 Coffee & Registration — Arrival, registration and informal networking before the workshop starts.
09:00 – 09:15 Opening and Introduction Siamak Farshidi Welcome, workshop objectives, and overview of the AI4RSE workshop program.
09:15 – 09:45 Beyond Automation: How AI is Transforming Research Software Engineering Prof. Bedir Tekinerdogan
Information Technology Group, Wageningen University
Introduction of the AI4RSE quadrant model and a research agenda for AI-augmented research software engineering.
09:45 – 10:15 eScience View on AI & RSE Dr. Carlos Martínez-Ortiz
Netherlands eScience Center
Experiences and lessons learned applying AI in research projects from an eScience perspective.
10:15 – 10:30 Coffee Break — Refreshments and informal discussions.
10:30 – 11:00 Challenges and Opportunities in Creating a Digital Orchard Dr. Bastiaan Boom
ActiveAI Group, OnePlanet Research Center (imec)
AI, sensor fusion and digital twins for next-generation orchard management.
11:00 – 11:30 Enhancing Research Software Quality in a Virtual Research Environment Dr. Zhiming Zhao
University of Amsterdam
Research Software Quality toolkit (RSQKit) and its use in Virtual Research Environments.
11:30 – 12:00 AI for Food Safety dr.ir. Bas van der Velden
Wageningen Food Safety Research
AI applications in chemical, biological, and image-based food safety monitoring.
12:00 – 12:30 Questionnaire and Group Setup Önder Babur Survey participants, form thematic groups, and assign facilitators for the afternoon tracks.
12:30 – 13:30 Lunch Break & Networking — Lunch and informal networking across groups and communities.

Afternoon Session

Parallel interactive sessions in three tracks, followed by a joint plenary and closing.

Time Session / Talk Track facilitators Location Notes
13:30 – 15:00 Parallel Interactive Sessions (3 Tracks) Participants choose one of three sessions, each including pitch preparation.
Track 1 – AI4RSE: Organization & Management Siamak Farshidi,
Ayalew Kassahun,
Önder Babur
B0075 Organizational and managerial aspects of AI4RSE and research software practices.
Track 2 – Using AI4RSE Tools Ebo Kwabena Bennin
Tahir Abbas
B0078 Introduction and guided use of tools and metrics for assessing research software.
Track 3 – Vibe Coding Carlos Martínez-Ortiz,
Mateusz Kuzak,
Faruk Diblen
B0073 Exploration of AI-assisted and collaborative coding workflows.
15:00 – 15:30 Coffee Break — B0075 Informal networking and preparation for plenary pitches.
15:30 – 16:00 Plenary Session – Group Pitches & Discussion All track facilitators B0075 Short pitches from each track and joint discussion of outcomes and recommendations.
16:00 – 16:15 Closing & Next Steps Ebo Kwabena Bennin B0075 Closing remarks, reflections, and call for follow-up collaboration.
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