Related papers: Integrative biological simulation praxis: Consider…
Epidemiologists have a growing interest in employing computational approaches to solve analytic problems, with simulation being arguably the most accessible among all approaches. While previous literature discussed the utility of simulation…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal…
This philosophical paper explores the relation between modern scientific simulations and the future of the universe. We argue that a simulation of an entire universe will result from future scientific activity. This requires us to tackle…
Unlike any other field, the science of morality has drawn attention from an extraordinarily diverse set of disciplines. An interdisciplinary research program has formed in which economists, biologists, neuroscientists, psychologists, and…
It is essential to find new ways of enabling experts in different disciplines to collaborate more efficient in the development of ever more complex systems, under increasing market pressures. One possible solution for this challenge is to…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
The aim of this review is to highlight the possibility to apply the mathematical formalism and methodology of quantum theory to model behaviour of complex biosystems, from genomes and proteins to animals, humans, ecological and social…
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
Scientific research involves mathematical modelling in the context of an interactive balance between theory, experiment and computation. However, computational methods and tools are still far from being appropriately integrated in the high…