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Cells In Sillico – Parallel Tissue Development Simulation

Berghoff, Marco


Insights in cell dynamics and tissue development are constantly changing our understanding of fundamental biological processes including embryogenesis, wound healing, and tumorigenesis. The availability of high-quality microscopy data and an increasing understanding of single-cell effects are speeding up discoveries. However, many computational models still describe either a few cells in high detail or larger cell ensembles and tissues in rather coarse detail. We combine these two scales, therefore we developed a highly parallel version of the cellular Potts model and provides an agent-based model for controlling cellular events. The model can be modularly extended to a multimodel simulation at both scales. Based on the NAStJA framework, we implemented a scalable version that runs efficiently on high-performance computing systems. Our model scales beyond 10,000 cores in an approximately linear manner, enabling the simulation of large three-dimensional tissues. The strictly modular design allows flexible configuration of arbitrary models and enables applications in a wide range of research questions. Cells in Silico can be easily adapted to different modeling assumptions and helps computational scientists to extend their simulations to a new area of tissue simulations. ... mehr

Volltext §
DOI: 10.5445/IR/1000135057
Veröffentlicht am 06.07.2021
Cover der Publikation
Zugehörige Institution(en) am KIT Scientific Computing Center (SCC)
Universität Karlsruhe (TH) – Zentrale Einrichtungen (Zentrale Einrichtungen)
Publikationstyp Vortrag
Publikationsdatum 16.06.2021
Sprache Englisch
Identifikator KITopen-ID: 1000135057
HGF-Programm 46.21.01 (POF IV, LK 01) Domain-Specific Simulation & SDLs and Research Groups
Veranstaltung Society for Mathematical Biology - Annual Meeting (SMB 2021), Online, 13.06.2021 – 17.06.2021
KIT – Die Forschungsuniversität in der Helmholtz-Gemeinschaft
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