We further integrated core CERN technologies into BioDynaMo. ROOT Notebooks provide life scientists with a web-based interface for (i) creating, running and visualising simulations, (ii) performing powerful analysis, and (iii) working interactively with a graphical user interface. Furthermore, users are now able to explore a large model parameter space on distributed computing infrastructures (e.g. cloud computers and computer clusters).
Based on feedback from our users, we improved BioDynaMo’s API. Now, life-scientists can translate an idea into a simulation faster than before. We were also able to connect BioDynaMo with another simulator, to benefit from the strengths of agent-based and continuum-based modelling for cancer research.
In addition, we succeeded in integrating systems biology markup language (SBML) into BioDynaMo. This makes it possible for life scientists to reuse the large database of existing SBML models to simulate chemical reaction networks within each BioDynaMo simulation object.
Finally, BioDynaMo was featured in CERN's official teachers and students programme in 2019. Teachers and students from Dutch high schools learned through hands-on sessions how ICT technologies developed at CERN help in tackling challenges in the biomedical fields.
BioDynaMo is currently able to simulate millions of cells on one server. To improve the performance yet further, we will focus on two main aspects. First, we will continue development on the distributed runtime, to combine the computational resources of many servers. Second, we will improve hardware acceleration to fully utilise (multiple) GPUs in a system. This will not only reduce runtime on high-end systems, but will also benefit users that work on a standard desktop or laptop.
Finally, thanks to new projects funded by the UK Engineering and Physical Sciences Research Council and the UK Medical Research Council in 2019, BioDynaMo has been extended for applications related to cryopreservation and the representation of realistic neural networks. Work in these areas will continue in 2020.