Related papers: Integrative biological simulation praxis: Consider…
Computing in the life sciences has undergone a transformative evolution, from early computational models in the 1950s to the applications of artificial intelligence (AI) and machine learning (ML) seen today. This paper highlights key…
Although simulation represents a major advance in the understanding of problems in complex systems, the field currently does not has standards in place that would guide the reporting of the data underlying each model, the process for model…
It has been proposed that human physical reasoning consists largely of running "physics engines in the head" in which the future trajectory of the physical system under consideration is computed precisely using accurate scientific theories.…
A central goal of Introductory Physics for the Life Sciences (IPLS) is to prepare students to use physics to model and analyze biological situations, a skill of increasing importance for their future studies and careers. Here we report our…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures…
The rapidly increasing interest in the quantum properties of living matter stimulates a discussion of the fundamental properties of life as well as quantum mechanics. In this discussion often concepts are used that originate in philosophy…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Conservation science is an interdisciplinary field that primarily draws on knowledge from the natural sciences, social sciences, and humanities to inform policy, planning, and practice. Since its formalization as a discipline, conservation…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
Frequently in socio-environmental sciences, models are used as tools to represent, understand, project and predict the behaviour of these complex systems. Along the modelling chain, Good Modelling Practices have been evolving that ensure -…
Despite the accelerating presence of exploratory causal analysis in modern science and medicine, the available non-experimental methods for validating causal models are not well characterized. One of the most popular methods is to evaluate…
The article deals with the problem of intellectual development of students in learning of physics by means of computer simulation. The main objectives of teaching computer simulation in learning of physics is the general outlook…
This paper investigates the reproducibility of computational science research and identifies key challenges facing the community today. It is the result of the First Summer School on Experimental Methodology in Computational Science…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel…
Biological and artificial information processing systems form representations of the world that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the similarity between the representations formed by…
The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they…