Workshops Thursday 17 October
CropXR education: what is coming up and how can you get involved?
Atoesa Farokhi, Ben Noordijk, Elysa Overdijk
The workshop focused on the development of educational modules for CropXR. The workshop moderators were excited to observe strong interest and enthusiasm from all participants. The discussions revolved around three main themes: how to transfer knowledge, the content of the education, and the skills needed. The workshop provided valuable insights that will be integrated into the education modules and the forthcoming university minor.
When discussing the topic of how to transfer knowledge, the participants of the workshop had different perspectives. Some emphasized the importance of a modular approach, suggesting that content should be offered as small “packages” or subtopics. This would enable other institutes to easily integrate these subtopics into their existing programs. Others, however, warned that separating subtopics in such way can compromise the interdisciplinary nature of the program. Whereas this is a strength. The participants deliberated a hybrid approach. Furthermore, the challenge of collaborating with companies was discussed. Participants suggested to formalize such partnerships and using real-world company cases. These could then be turned into structured learning materials, which could be shared across institutions.
In terms of content, the group highlighted the need to combine biological and technical knowledge with ethical and social considerations. Key topics include plant genomics, breeding, and the connection between genotype and phenotype. However, understanding the social-economic impacts, such as whether farmers will adopt new seeds, and considering ethical concerns about new genomic techniques, is equally important. Participants stressed the importance of reflexivity. It is particularly important to consider the perspectives of farmers, consumers, and the broader political economy, as well as our shared responsibility in feeding the world.
When discussing skills, the emphasis was on fostering essential soft skills that are often neglected in academic settings. These include project management, effective communication, and an understanding of team dynamics. Participants also highlighted the need for reflexivity—being aware of different perspectives and listening to others. Social skills, such as the ability to communicate across disciplines and with stakeholders like farmers and companies, are critical for the success of these modules. The workshop leaders will take all this input into account. They will incorporate it into the development of both the modules and the minor during our monthly minor working sessions. If you have any further suggestions, please feel free to contact Atoesa Farokhi. Lastly: soon the minor’s promotional materials, which will begin in September 2025, will be shared with the community.
Plant resilience for non-biologists
Martijn van Zanten
In this workshop the workshop leader highlighted that plants are not helpless creatures. Despite being sessile, plants master the art of being flexible. The workshop was held in two recurrent sessions.
The first session was attended mostly by non-biologist. The focus of this session was on the diverse strategies plants possess to cope with adverse environmental conditions. The participants discussed the differences and commonalities between evolutionary adaptations to cope with stress and how phenotypic plasticity aids resilience. Examples were showcased of diverse strategies: i) adaptation (for instance needles of cacti), ii) acclimation (stop, adjust and continue), iii) escaping the limiting abiotic factor (shade- and submergence avoidance), iv) engagement strategies through tropisms and v) tolerating the stressful situation (quiescent strategy of for instance certain rice cultivars when submerged).
The second session was attended mostly by biologist from academia and industry. The same examples were discussed, but in addition, the participants debated how stress dose determines the resilience strategy of the plant. In addition, they discussed how resilience is affected by breeding and domestication. The group concluded that desired stress resilience of a managed crop can be different from the resilience potential a natural plant requires in the wild. Moreover, the group embarked on the discussion how the CropXR community can incorporate the existing wealth of phenotypic data on crops across stress gradients into research on plant stress resilience within the context of CropXR. Since the current focus of CropXR is largely on genetic and molecular data. For instance, how can we benefit from decades of wheat and maize research across temperature gradients? This data that is readily available.
In both sessions the participants started a discussion on how the CropXR community should define plant resilience in the context of CropXR. Furthermore, it was discussed if we should work with different definitions depending on the stakeholder and desired outcomes. It became clear that this discussion is not yet settled. The groups concluded that this would be an interesting topic for a workshop or a pressure cooker session at the next CropXR conference.
Modeling and AI for biologists
Jordan Earle, Jordi Alonso Esteve, Aalt-Jan van Dijk
In the workshop “AI and modelling for plant biologists” the workshop leaders focused on the use of machine learning (ML) and mechanistic models in biology. The intended audience consisted of plant science researchers without much experience or affinity with computational research. The goal of the workshop was to demonstrate how these computational methods can be applied to address biological questions, in particular related to plant resilience.
The workshop began with a presentation discussing key aspects of ML and mechanistic models. This was followed by interactive demonstrations, where participants had the opportunity to experiment with an online deep learning tool. There was a lot of enthusiasm among the participants, especially when trying out the online tool for deep learning, where different settings were tested to observe their impact on model performance.
Throughout the workshop, group discussions were held, during which participants explored which biological mechanisms are relevant to their own research and how ML or mechanistic models could be used to describe these processes. Several suggestions were made on how these methods could be employed to improve plant resilience, and what would be key factors to take into account, such as modeling stress factors and predicting responses to environmental changes.
At the end of the workshop, a brief discussion focused on the potential to link a mechanistic model and an ML model which are currently being developed in WP.C2. Participants shared ideas on how an integrated approach could be useful for these models. The workshop concluded with the recognition that collaboration between modelers and biologists is essential for successful model development, and that further integration of ML and mechanistic models offers new opportunities to tackle biological challenges.