New computational platform to study biological processes

Date:
September 20, 2021
Source:
University of Surrey
Summary:
Scientists have launched a unique software that is able to perform
highly complex simulations of a variety of biological processes.



FULL STORY ========================================================================== Scientists have launched a unique software that is able to perform highly complex simulations of a variety of biological processes.


========================================================================== Agent-based simulations (ABS) are powerful computational tools that help scientists understand complex biological systems. These simulations are
an inexpensive and efficient way to quickly test hypotheses about the physiology of cellular tissues, organs, or entire organisms. However,
many ABS do not take full advantage of available computational power,
and the majority of ABS platforms on the market are designed with a
particular use case in mind.

In a paper published by Bioinformatics, a consortium that includes the University of Surrey, CERN, Newcastle University, GSI Helmholtz Centre, University of Cyprus, University of Geneva, SCImPULSE Foundation and Immunobrain Checkpoint, unveil their open-source, multi-disciplinary
simulation platform called BioDynaMo.

In the paper, the consortium details how BioDynaMo can simulate complex
medical cases in neuroscience, oncology, and epidemiology, thanks to its ability to utilise multi-core CPUs and offload computations to hardware accelerators.

The team's results show that BioDynaMo performs up to 945 times faster
than current state-of-the-art baselines. The advances make it feasible
to simulate each use case with one billion cells on a single server,
showcasing the potential BioDynaMo has for computational biology research.

Dr Roman Bauer from the University of Surrey, co-founder of the BioDynaMo initiative and senior author of the study, said: "I believe that if
we are ever to tackle highly complex health issues such as Alzheimer,
computer simulation tools like BioDynaMo will be critical for scientists
moving forward.

"In this paper, we have shown that BioDynaMO's excellent features
and performance. It will help the scientists of tomorrow pitting
hypotheses against each other to study their subtle or less
so divergences. And more importantly, it will help biomedical
research become a truly interdisciplinary field of the 21st century." ========================================================================== Story Source: Materials provided by University_of_Surrey. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios
Vavourakis,
Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca,
Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu,
Roman Bauer. BioDynaMo: a modular platform for high-performance
agent-based simulation.

Bioinformatics, 2021; DOI: 10.1093/bioinformatics/btab649 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/09/210920121741.htm

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