BioDynaMo in 2024 - End of the year remarks, and Holidays greetings

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:

  1. 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
  2. Also in the domain of oncology, a study leveraged BioDynaMo to simulate vascular tumour growth, with a focus on breast cancer. The authors demonstrated how the model can be utilised to inform on breast cancer treatment options. Find out more here:
    https://www.sciencedirect.com/science/article/pii/S0045782523006904
  3. A neuroscientific paper demonstrating how BioDynaMo, in conjunction with Bayesian statistics, can be used to generate highly realistic neurons in 3D. Notably, the neuronal morphologies are generated mechanistically via concrete growth rules. Such models improve our understanding of brain development and can help inform stem-cell based therapies to regenerate parts of the brain. Find the paper here:
    https://link.springer.com/article/10.1007/s00285-024-02144-2
  4. One of the major questions when it comes to designing agent-based models is with regards to identifying suitable parameters, and avoiding over-fitting. A paper from BioDynaMo members, addressing various aspects of parameter calibration in agent-based modelling is available here:
    https://www.tandfonline.com/doi/full/10.1080/15384047.2024.2344600
  5. Lukas successfully defended his PhD viva at ETH Zurich, with his thesis work titled “Design and Analysis of an Extreme-Scale, High-Performance, and Modular Agent-Based Simulation Platform”. Congratulations Dr Breitwieser!
  6. As part of our ongoing training and educational initiatives, we provided an online tutorial on BioDynaMo for the NETSKINMODELS EU COST Action.
  7. BioDynaMo member University of Surrey produced a promotional video, featuring our very own Roman describing use cases and expressing a call to action for interdisciplinary collaboration: https://www.youtube.com/watch?v=MS_idphAa8k
  8. We organised multiple hybrid meetings that included speakers talking about BioDynaMo and its applications (see for instance https://www.combynelab.com/home/news/combiohealth_nov2024)


We would like to extend our deepest gratitude to each BioDynaMo member for your hard work, creativity and dedication. It is your contributions that make our collaboration not only productive but also enjoyable. Thank you for your professionalism and for the camaraderie that we have built over the year.

As we celebrate this year’s achievements (and apologies for not being able to bring up all!) and prepare for the challenges ahead, we encourage each of you to reflect on your individual contributions and to recharge over the holiday season. We are excited about what we can accomplish together in the upcoming year. Along those lines, we welcome our recent joiners, Mr Stavros Portokalidis at CERN, and Mr Ioannis Papadopoulos at University of Cyprus / University of Surrey.

Obviously, we also need to look forward and face upcoming events. We’d like to refer to the ESB mini-symposium that we are organizing with other relevant scientists: https://esbiomech2025.org/. If you are interested or have colleagues/collaborators who may be interested, please spread the word.

Moreover, Roman is co-organising a workshop at the prestigious IEEE Conference on AI in Santa Clara, California, USA on June 5th to 7th, 2025. The topic is “AI for Biology and Biomedicine”. Paper submissions are due by the 15th of January. More information is available here:
https://www.combynelab.com/home/news/ai_for_biology_and_biomedicine_2025

Further opportunities are in meetings with the NetBioMed satellite at the International School and Conference on Network Science in Maastrich, Netherlands on June 2nd to 6th, 2025: https://netsci2025.github.io/satellites/

We’d also like to bring up that as an open-source software collaboration we need to rely on contributions from generous and committed members who generously support and help maintain the code, as well as help new joiners with issues. Information on how to contact us can be found here: https://www.biodynamo.org/contacts-us/support-biodynamo. At this point, we’d like to say a big thank you to those members who have done this during the year, and particularly Tobias Duswald who arguably again (!) provided the most active support!

We wish you a joyful holiday season and a prosperous New Year!

Warm regards,
Roman, Vasilis and Marco

Comments

Post a Comment

Popular posts from this blog

Modelling lung cells to personalize radiotherapy (with BioDynaMo) among the Top 10 Breakthroughs of the Year in physics for 2024!

Image
 Last December the 12th Physics World has delighted announced its Top 10 Breakthroughs of the Year for 2024, which includes research in nuclear and medical physics, quantum computing, lasers, antimatter and (of course ^_^) BioDynaMo . The Top Ten is the shortlist for the Physics World Breakthrough of the Year, which will be revealed on Thursday 19 December. PhysicsWorld editorial team has looked back at all the scientific discoveries reported on since 1 January and has picked 10 they judge are the most important. In addition to being reported in Physics World in 2024, the breakthroughs must meet the following criteria:  Significant advance in knowledge or understanding Importance of work for scientific progress and/or development of real-world applications Of general interest to Physics World readers  You can listen to the editors making their case for the research in the Top10 in this podcast What do they say about the BioDynaMo research they selected: <<Modelling...
Read more

Using BioDynaMo to Study Virus Spread in Closed Environments

 In addition to cellular studies (tumour growth modelling or neural development), BioDynaMo can be used to simulate different systems, such as groups of people and their interactions. As BioDynaMo has been developed to simulate billions of cells, it should be able to handle fairly easily simulations of up to millions of people. In one of these types of simulation, BioDynaMo is used to study the spreading of viruses in indoor spaces, specifically COVID-19 in droplets and aerosols. We are investigating several scenarios, such as public transportation (bus, metro) and buildings (supermarkets, offices). In these simulations BioDynaMo is in charge of simulating the behaviour and characteristics of individuals, while the ROOT geometrical modeller is used to define the precise environmental geometry. Each individual can then independently move around in these environments where infected individuals can possibly contaminate healthy ones through the spreading of droplets and aerosols. By st...
Read more