Related papers: Integrative biological simulation praxis: Consider…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
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…
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome,…
Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses computational models to perform complex experiments that are…
This paper provides the first systematic philosophical analysis of an increasingly important part of modern scientific practice: analogue quantum simulation. We introduce the distinction between `simulation' and `emulation' as applied in…
Life, services and activities within cities have commonly been studied by separate disciplines, each one independent from the others. One such approach is the computer simulation, which enables in-depth modelling and cost-effective…
Motivated by the current demand of clinical governance, surgical simulation is now a well-established modality for basic skills training and assessment. The practical deployment of the technique is a multi-disciplinary venture encompassing…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a…
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…
Computational psychiatry is a field aimed at developing formal models of information processing in the human brain, and how alterations in this processing can lead to clinical phenomena. Despite significant progress in the development of…
At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…
Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
Educators and policy-makers have advocated for reform of undergraduate biology education, calling for greater integration of mathematics and physics in the biology curriculum. While these calls reflect the increasingly interdisciplinary…
Different research communities have developed various approaches to assess the credibility of predictive models. Each approach usually works well for a specific type of model, and under some epistemic conditions that are normally satisfied…
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…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…