Project goal

We’re 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
Collaborator liaison(s)
Roman Bauer (Newcastle University), Claudio Bellini (Intel), Marcus Kaiser (Newcastle University), Manuel Mazzara (Innopolis Univesity), Klaus-Dieter Oertel (Intel), Max Talanov (Kazan Federal University)

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, Innopolis University in Russia, and Kazan Federal University in Russia, and Intel. Together, we are working to develop a unique platform.

Recent progress

Throughout 2017, we worked on improving the code base to harness fully the capabilities of modern hardware. With its improved modular architecture, BioDynaMo is now ready for use in a range of different biological fields. The integration of ParaView — a popular scientific visualisation engine — into the platform was an important milestone. This enables life scientists to visualise and interact with their simulation, even as it is running.

Backup-and-restore functionality is essential, particularly for simulations that take longer to run. We therefore integrated ROOT — a data-processing framework created at CERN and used widely in the high-energy physics community — into the BioDynaMo platform. At CERN, ROOT is used to store the large amount of data produced by the LHC experiments; it also enables fast post-processing and analysis of data.

It is also very important that the platform is user friendly: we spent significant effort improving the installation and usage experience. It is now possible to set up BioDynaMo and run a simulation in just three simple steps. During 2017, we also laid the foundations for running BioDynaMo in the cloud. Using distributed computing will make it possible to harness many thousands of computer processors to simulate very large biological structures.

Next steps

Being able to run simulations on multiple compute nodes in parallel is essential for complex modelling. Consequently, our next milestone is to complete the distributed runtime for BioDynaMo. We will also investigate ways to mitigate the I/O bottleneck in low-bandwidth, high-latency environments and to take advantage of heterogeneous computing.

Publications

  • L. Breitwieser, BioDynaMo: A New Platform for Large-Scale Biological Simulation (Master’s thesis), Graz University of Technology, Austria, 2016. http://cern.ch/go/z67t

Presentations

  • K. Kanellis, Scaling a biological simulation platform to the cloud (15 August), Presented at CERN openlab summer students’ lightning talks, Geneva, 2017. http://cern.ch/go/d9nV
  • L. Breitwieser, BioDynaMo (21 September), Presented at CERN openlab Open Day, Geneva, 2017. http://cern.ch/go/lNP9
  • L. Breitwieser & A. Hesam, BioDynaMo: Biological simulation in the cloud (1 December), Presented at CERN IT technical forum, Geneva, 2017. http://cern.ch/go/m9Kw