BioDynaMo

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
Applications in other disciplines
Project coordinator(s)
Fons Rademakers
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 and other institutions, 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.

ImmunoBrain Checkpoint, GSI Darmstadt and the University of Cyprus are also collaborating in BioDynaMo. Find out more about the project on the collaboration page: biodynamo.org/.

Recent progress

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.

Next steps

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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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
    L. Breitwieser, R. Bauer, A. Di Meglio, L. Johard, M. Kaiser, M. Manca, M. Mazzara, F. Rademakers, M. Talanov, The BioDynaMo project: Creating a platform for large-scale reproducible biological simulations. CEUR Workshop Proceedings, 2016. cern.ch/go/Xv8l
    R. Bauer, L. Breitwieser, A. Di Meglio, L. Johard, M. Kaiser, M. Manca, M. Mazzara, F. Rademakers, M. Talanov, A. D. Tchitchigin, The BioDynaMo project: experience report. In Advanced Research on Biologically Inspired Cognitive Architectures (pp. 117-125). IGI Global, 2017. cern.ch/go/dp77
    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. cern.ch/go/f9v6
    J. de Montigny, A. Iosif, L. Breitwieser, M. Manca, R. Bauer, V. Vavourakis, An in silico hybrid continuum-/agent-based procedure to modelling cancer development: interrogating the interplay amongst glioma invasion, vascularity and necrosis. Methods, 2020. cern.ch/go/6vrm

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. 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. 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. 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. cern.ch/go/kJv7
    L. Breitwieser, BioDynaMo (23 January). Presented at CERN openlab workshop, Geneva, 2019. cern.ch/go/7RlF
    R. Bauer, Computational modelling and simulation of biophysical dynamics in medicine (7 June). Presented at Big Data in Medicine: Challenges and Opportunities, Geneva, 2019. cern.ch/go/xf9F
    F. Rademakers, BioDynaMo (20 June). Presented at Hôpitaux Universitaires de Genève, Geneva, 2019.
    J. L. Jennings, Computational Modelling of cryopreservation using the BioDynaMo software package CryoDynaMo (22 July). Presented at the Society for Cryobiology Conference, San Diego, 2019.
    J. de Montigny, Computational modelling of retinal ganglion cell development (July). Presented at UK Neural Computation, Nottingham, 2019.
    G. De Toni, Improvements on BioDynaMo Build System (13 August). Presented at the CERN openlab summer student lightning talk session, Geneva, 2019. cern.ch/go/xt68
    G. De Toni, Improvements on BioDynaMo Build System (13 August). Presented at the CERN openlab summer student lightning talk session, Geneva, 2019. cern.ch/go/xt68
    L. Breitwieser, BioDynaMo Project Update (26 September). Presented at CERN Medical Application Project Forum, Geneva, 2019.
    A. Hesam, Simulation Master Class (26 September). Presented at CERN's Dutch Language Teachers Programme, Geneva, 2019. cern.ch/go/hKL7
    A. Hesam, Simulation Master Class (11 October). Presented at CERN's Dutch Language Students Programme (NVV Profielwerkstukreis), Geneva, 2019.
    L. Breitwieser, A. Hesam, The BioDynaMo Project (21 October). Presented at EmLife Meeting, Geneva, 2019.
    L. Breitwieser, The BioDynaMo Software Part I (2 December). Presented at the BioDynaMo Collaboration Meeting, Zurich, 2019.
    A. Hesam, The BioDynaMo Software Part II (2 December). Presented at the BioDynaMo Collaboration Meeting, Zurich, 2019.
    R. Bauer, BioDynaMo: A platform for computational models and simulations of biological systems, Presented at CERN Knowledge Exchange Event, Daresbury, 2019.