Related papers: The BioDynaMo Project
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results:…
The ubiquitous presence of computer simulations in all kinds of research areas evidence their role as the new driving force for the advancement of science and engineering research. Nothing seems to escape the image of success that computer…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Dynamo is a full-stack software solution for scientific data management. Dynamo's architecture is modular, extensible, and customizable, making the software suitable for managing data in a wide range of installation scales, from a few…
Progress in science is deeply bound to the effective use of high-performance computing infrastructures and to the efficient extraction of knowledge from vast amounts of data. Such data comes from different sources that follow a cycle…
The enabling of scientific experiments that are embarrassingly parallel, long running and data-intensive into a cloud-based execution environment is a desirable, though complex undertaking for many researchers. The management of such…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Computational experiments have become essential for scientific discovery, allowing researchers to test hypotheses, analyze complex datasets, and validate findings. However, as computational experiments grow in scale and complexity, ensuring…
Scientific computing applications have benefited greatly from high performance computing infrastructure such as supercomputers. However, we are seeing a paradigm shift in the computational structure, design, and requirements of these…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
A key element of the European Union's Human Brain Project (HBP) and other large-scale brain research projects is simulation of large-scale model networks of neurons. Here we argue why such simulations will likely be indispensable for…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
A significant amount of high-impact contemporary scientific research occurs where biology, computer science, engineering and chemistry converge. Although programmes have been put in place to support such work, the complex dynamics of…
Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to…
Cloud computing provides a great opportunity for scientists, as it enables large-scale experiments that cannot are too long to run on local desktop machines. Cloud-based computations can be highly parallel, long running and data-intensive,…
In the world of Information Technology, new computing paradigms, driven by requirements of different classes of problems and applications, emerge rapidly. These new computing paradigms pose many new research challenges. Researchers from…
Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…