BioDynaMo collaboration

 Interested in AI and biology? Then this PhD studentship could be for you! Thousands of donated organs are discarded each year because current preservation methods allow storage for only a few hours. Cryopreservation at ultra-low temperatures offers the prospect of long-term organ banking, but its application to large tissues and organs is limited by ice crystal formation and the toxicity of existing cryoprotective agents (CPAs). Overcoming these challenges is a major unmet need in biomedicine. This interdisciplinary PhD project aims to develop AI-driven approaches to discover safer and more effective CPAs by integrating machine learning, computational modelling, and experimental validation. The successful candidate will receive training in both computational and experimental biology within a highly collaborative research environment. The project will begin with the construction of a curated database from the literature, capturing known CPAs, their properties, concentrations, and ...

 New computer modelling could help scientists better understand how the retina regenerates, opening the door to new treatments for vision loss, according to a study from the University of Surrey.  " My left eye retina " by Richard Masoner / Cyclelicious is licensed under CC BY-SA 2.0 . The first-of-its-kind model is capable of detailing how the retina – the light-sensitive layer at the back of the eye – can build its complex structure from just one type of stem cell, deepening our understanding of how sight develops and how its development could inform studies of injury or disease.  Using advanced agent-based modelling, the research team have simulated key stages of retinogenesis – the process by which identical progenitor cells diversify into the six types of neurons that make up the retina.  The model shows how simple genetic rules and subtle randomness work together to form the retina’s precise layered architecture, a structure essential for how we see.  The...

 Our new paper on computational modelling and AI in dermatology , published with an outstanding team of collaborators from five countries 🌍 . This review explores how in silico approaches – from data-driven methods to model-based simulations – are transforming dermatology by offering new insights into skin biology, disease mechanisms, and therapeutic strategies.  We highlight advances such as virtual skin models, skin-on-chip devices, and computational tools for surgical planning, while also discussing the challenges that remain around data, validation, and interdisciplinary collaboration.  Excited about the opportunities this growing field holds for biomedical research and clinical innovation!  Thanks to the European NETSKINMODELS COST Action for making this collaboration possible!   Read the manuscript ( it's open access of course ! ) and discover our stellar authors' team by clicking on their names to open their profiles Ceylan S , Demir D , Harris C ,...

   NetBioMed , a satellite of the NetSci conference , in their own words brings together researchers on Machine Learning, Digital Twins and Complex Systems towards solving problems in biology and medicine . On June the 2nd 2025  Dr Marco Manca  (President of SCImPULSE Foundation ) has joined friends and colleagues from around the world to discuss the epistemology of life sciences. In an intense half an hour talk, Dr Manca has lead the audience through a brief history of delusions in medical knowledge, to immediately focus on the processes and pitfalls of building human knowledge, the impact of assumptions (dscussing the case of ergodicity assumptions) and models on measurements (and thus, on data). He discussed the pros and cons of machine learning and the limitations of the aspiration to extract "objective knowledge" from data, or even dependable knowledge, because of the very founding principles on which ML as we have it today works. He then mo...

 Our spokesperson  Dr Bauer 's research focusses on the computational modelling and analysis of biological dynamics, in particular those of the brain. His highly interdisciplinary research involves modern computing approaches, biological expertise, innovative machine learning methods and IT- related collaboration, as we know. As you probably remember, Dr Bauer has been a 2024 Fellow of the Foresight Institute  and thus, he has had the opportunity to share his reflections about computational biology with a wider audience of brilliant people. Here we share two of his recent interviews/lectures, of course on topics we hold very dear. 1) Computational Modeling in Biomedicine: With the Eggs in Multiple Baskets Abstract :  Computational modeling is one of the pillars of the scientific method. Unsurprisingly, it has also become paramount for biomedical research when it entails various data modalities and numerous biological, physical and chemical processes. Moreover, t...

Dear all,  as we are approaching the end of 2024, we would like to take a moment to reflect on our collaborative achievements within the BioDynaMo community. It has been a year marked by innovation, resilience, and shared commitment to advancing our understanding of various biological systems through innovative computational modelling. This year, the consortium had several important successes. We would like to specifically mention/highlight: The paper presenting BioDynaMo’s application to cancer treatment. Radiation-induced fibrosis is a major risk factor in radiotherapy for lung cancer patients. BioDynaMo members including our Nicolo as first author published in the very prestigious Nature Communications Medicine journal, showing how BioDynaMo can be used to simulate the impact of radiation on the lung on a single cell level. Such modelling can be used to improve radiotherapy: https://www.nature.com/articles/s43856-024-00442-w Also in the domain of oncology, a study leve...