Related papers: The BioDynaMo Project
High-performance scientific applications require more and more compute power. The concurrent use of multiple distributed compute resources is vital for making scientific progress. The resulting distributed system, a so-called Jungle…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…
Numerical simulation of quantum systems is crucial to further our understanding of natural phenomena. Many systems of key interest and importance, in areas such as superconducting materials and quantum chemistry, are thought to be described…
Powered by advanced information technology, more and more complex systems are exhibiting characteristics of the Cyber-Physical-Social Systems (CPSS). Understanding the mechanism of CPSS is essential to our ability to control their actions,…
Computerization of research activities led to the creation of large specialized information resources, platforms, services and software to support scientific research. However, their shortcomings do not allow to fully realizing the…
The ever increasing demands placed upon machine performance have resulted in the need for more comprehensive particle accelerator modeling. Computer simulations are key to the success of particle accelerators. Many aspects of particle…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
The recent attention towards research and development in cyber-physical energy systems has introduced the necessity of emerging multi-domain co-simulation tools. Different educational, research and industrial efforts have been set to tackle…
Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As…
This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the…
The rapid advancements in quantum computing necessitate a scientific and rigorous approach to the construction of a corresponding software ecosystem, a topic underexplored and primed for systematic investigation. This chapter takes an…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
In the dawn of computer science and the eve of neuroscience we participate in rebirth of neuroscience due to new technology that allows us to deeply and precisely explore whole new world that dwells in our brains.
Computing devices are vital to all areas of modern life and permeate every aspect of our society. The ubiquity of computing and our reliance on it has been accelerated and amplified by the COVID-19 pandemic. From education to work…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
Some common systems modelling and simulation approaches for immune problems are Monte Carlo simulations, system dynamics, discrete-event simulation and agent-based simulation. These methods, however, are still not widely adopted in…
Scientific communities naturally tend to organize around data ecosystems created by the combination of their observational devices, their data repositories, and the workflows essential to carry their research from observation to discovery.…
At the frontier of most areas in science, computer simulations play a central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and…