Related papers: The BioDynaMo Project
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
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…
Cloud computing recently developed into a viable alternative to on-premises systems for executing high-performance computing (HPC) applications. With the emergence of new vendors and hardware options, there is now a growing need to…
The complexity of biological systems, governed by molecular interactions across hierarchical scales, presents a challenge for computational modeling. While advances in multiomic profiling have enabled precise measurements of biological…
Hybrid modeling combining data-driven techniques and numerical methods is an emerging and promising research direction for efficient climate simulation. However, previous works lack practical platforms, making developing hybrid modeling a…
With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…
Creation of the information systems and tools for scientific research and development support has always been one of the central directions of the development of computer science. The main features of the modern evolution of scientific…
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent,…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Scientific workflow has become essential in software engineering because it provides a structured approach to designing, executing, and analyzing scientific experiments. Software developers and researchers have developed hundreds of…
Scientific computing applications usually need huge amounts of computational power. The cloud provides interesting high-performance computing solutions, with its promise of virtually infinite resources on demand. However, migrating…
Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication…
Animal behavior reflects interactions between the nervous system, body, and environment. Therefore, biomechanics and environmental context must be considered to understand algorithms for behavioral control. Neuromechanical digital twins,…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
The challenge of translating vast, multimodal biological data into predictive and mechanistic understanding of cellular function is a central theme in modern biology. Virtual cells, or digital cellular twins, have emerged as a critical…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…