Project goal

We are aiming to create a platform through which life scientists can easily create, run, and visualise three-dimensional biological simulations. Built on top of the latest computing technologies, the BioDynaMo platform will enable users to perform simulations of previously unachievable scale and complexity, making it possible to tackle challenging scientific research questions.

R&D topic
R&D Topic 4: Applications in other disciplines
Project coordinator(s)
Fons Rademakers
Technical team members
Lukas Breitwieser, Ahmad Hesam, Klaus-Dieter Oertel
Collaborator liaison(s)
Roman Bauer (Newcastle University), Claudio Bellini (Intel)

Collaborators

Project background

Within the life-sciences community, computer simulation is being used more and more to model increasingly complex biological systems. Although many specialised software tools exist, establishing a high-performance, general-purpose platform would be a major step forward. CERN is therefore contributing its deep knowledge in large-scale computing to this collaboration with Newcastle University in the UK, supported by Intel. Together, we are working to develop a unique platform. This project is cofinanced by the CERN budget for knowledge transfer to medical applications.

Recent progress

In 2018, we added a neuroscience module that enables scientists to simulate the growth of dendrites — tree-like extensions of nerve cells — in 3D space. This made it possible for Jean de Montigny, a PhD student at Newcastle University, to use BioDynaMo to investigate retinal development. His research focuses on understanding the organisation of retinal ganglion cells, a type of neuron located near the inner surface of the retina. These cells are known for exhibiting semi-regular patterns of spatial arrangement, called retinal mosaics. Three main theories for retinal mosaic development exist. BioDynaMo is now being used to investigate these theories and the mechanisms that could influence the shape of these cells’ dendritic trees.

Work to further increase performance also continued in 2018. Preliminary testing shows a performance increase of an order of magnitude, comparing single-thread performance of BioDynaMo against the benchmark software. BioDynaMo is fully parallelised and also optimised for non-uniform memory architectures. Thus, it scales well with the number of physical cores within one compute node, even for servers with multiple sockets. In addition, we also explored the possibilities of using heterogeneous computing resources (GPU and FPGA) to further reduce simulation time.

Next steps

Although the current simulation engine exploits the parallelism of modern hardware within a single compute node, the complexity of the biological model that can be simulated is limited. We will therefore develop a scale-out architecture to distribute computations across many compute nodes in a cloud infrastructure.

Publications

    L. Breitwieser, BioDynaMo: A New Platform for Large-Scale Biological Simulation (Master’s thesis), Graz University of Technology, Austria, 2016. cern.ch/go/z67t
    A. Hesam, Faster than the Speed of Life: Accelerating Developmental Biology Simulations with GPUs and FPGAs (Master’s thesis), Delft University of Technology, Netherlands, 2018. http://cern.ch/go/f9v6

Presentations

    K. Kanellis, Scaling a biological simulation platform to the cloud (15 August), Presented at CERN openlab summer students’ lightning talks, Geneva, 2017. cern.ch/go/d9nV
    L. Breitwieser, BioDynaMo (21 September), Presented at CERN openlab Open Day, Geneva, 2017. cern.ch/go/lNP9
    L. Breitwieser & A. Hesam, BioDynaMo: Biological simulation in the cloud (1 December), Presented at CERN IT technical forum, Geneva, 2017. cern.ch/go/m9Kw
    A. Hesam, Biodynamo project status and plans (11 January). Presented at CERN openlab Technical Workshop, Geneva, 2018. http://cern.ch/go/F8Cl
    L. Breitwieser, BioDynaMo (1 February). Presented at University Hospital of Geneva Café de l'Innovation, Geneva, 2018.
    L. Breitwieser, The Anticipated Challenges of Running Biomedical Simulations in the Cloud (12 February). Presented at Early Career Researchers in Medical Applications @ CERN, Geneva, 2018. http://cern.ch/go/spc8
    N. Nguyen, Distributed BioDynaMo (16 August). Presented at CERN openlab summer students' lightning talks, Geneva, 2018.
    A. Hesam, Faster than the Speed of Life: Accelerating Developmental Biology Simulations with GPUs and FPGAs (31 August). Master’s thesis defense, Delft, 2018. http://cern.ch/go/f9v6
    L. Breitwieser, The BioDynaMo Project: towards a platform for large-scale biological simulation (17 September). Presented at DIANA meeting, Geneva, 2018. http://cern.ch/go/kJv7