Current research in the field of computational biology often involves simulations on high-performance computer clusters. It is crucial that the code of such simulations is efficient and correctly reflects the model specifications. In this paper, we present an optimization strategy for agent-based simulations of biological dynamics using Intel Xeon Phi coprocessors, demonstrated by a prize-winning entry of the “Intel Modern Code Developer Challenge” competition. These optimizations allow simulating various biological mechanisms, in particular the simulation of millions of cells, their proliferation, movements and interactions in 3D space. Overall, our results demonstrate a powerful approach to implement and conduct very detailed and large-sc...
Stochastic simulations of biochemical reaction networks can be computationally expensive on Central ...
Computational modelling of populations of cells has been applied to further understanding in a range...
総説・解説などインパクトファクター(0.94)被引用回数(4)Learning how biological systems solve problems could help to design n...
Researchers in biology are faced with the tough challenge of developing high-performance computer si...
Timothy is a novel large scale modelling framework that allows simulating of biological processes in...
We present optimisations applied to a bespoke biophysical molecular dynamics simulation designed to ...
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. H...
Molecular dynamics (MD) is a powerful computer simulation technique providing atomistic resolution a...
Abstract Mathematical modeling and computer simulation are important tools for understanding complex...
Understanding biological evolution prompts for a detailed understanding of the realized phenotype. B...
Abstract. Agent-based simulation of large multicellular biological sys-tems has become a viable opti...
Molecular dynamics is an important method for protein structure research, which is called the holy g...
The growing area of systems biology has been using agent-based models for many years with early mode...
Background In recent years, the study of immune response behaviour using bottom up approach, Agen...
Abstract—Special-purpose computing hardware can provide significantly better performance and power e...
Stochastic simulations of biochemical reaction networks can be computationally expensive on Central ...
Computational modelling of populations of cells has been applied to further understanding in a range...
総説・解説などインパクトファクター(0.94)被引用回数(4)Learning how biological systems solve problems could help to design n...
Researchers in biology are faced with the tough challenge of developing high-performance computer si...
Timothy is a novel large scale modelling framework that allows simulating of biological processes in...
We present optimisations applied to a bespoke biophysical molecular dynamics simulation designed to ...
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. H...
Molecular dynamics (MD) is a powerful computer simulation technique providing atomistic resolution a...
Abstract Mathematical modeling and computer simulation are important tools for understanding complex...
Understanding biological evolution prompts for a detailed understanding of the realized phenotype. B...
Abstract. Agent-based simulation of large multicellular biological sys-tems has become a viable opti...
Molecular dynamics is an important method for protein structure research, which is called the holy g...
The growing area of systems biology has been using agent-based models for many years with early mode...
Background In recent years, the study of immune response behaviour using bottom up approach, Agen...
Abstract—Special-purpose computing hardware can provide significantly better performance and power e...
Stochastic simulations of biochemical reaction networks can be computationally expensive on Central ...
Computational modelling of populations of cells has been applied to further understanding in a range...
総説・解説などインパクトファクター(0.94)被引用回数(4)Learning how biological systems solve problems could help to design n...