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The complexity of human biology and its intricate systems holds immense potential for advancing human health, disease treatment, and scientific discovery. However, traditional manual methods for studying biological interactions are often…
Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…
Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can…
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…
Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate…
BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…
Across biological subdisciplines, the last decade has seen an explosion of high-dimensional datasets, including datasets for cells, species, immune systems, neurons and behaviour. At the ICTS workshop 'Unifying Theories in High-Dimensional…
Mathematical and numerical modeling is an increasingly important, yet often neglected, topic for biology students. We have found Glowscript to facilitate teaching and introducing computer simulations to students. In particular, the built-in…
A practical guide for university academics who need to create learning materials that support flexible delivery methods. Examples from the Computer Science domain are used to illustrate innovative approaches to engaging students with online…
The application of high end computing to astrophysical problems, mainly in the galactic environment, is under development since many years at the Dep. of Physics of Sapienza Univ. of Roma. The main scientific topic is the physics of self…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified interface. Our framework is intrinsically parallel, and conveniently separates all component numerical modules in…
Much of the research done by modern physicists would be impossible without the use of computation. And yet, while computation is a crucial tool of practicing physicists, physics curricula do not generally reflect its importance and utility.…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Biological systems offer a great many examples of how sophisticated, highly adapted behavior can emerge from training. Here we discuss how training might be used to impart similarly adaptive properties in physical matter. As a special form…
Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries,…
We introduce HepLean, an open-source project to digitalise definitions, theorems, proofs, and calculations in high energy physics using the interactive theorem prover Lean 4. HepLean has the potential to benefit the high energy physics…
Numerical simulations are ubiquitous in mathematics and computational science. Several industrial and clinical applications entail modeling complex multiphysics systems that evolve over a variety of spatial and temporal scales. This study…
The discipline of `theoretical biology' has been developing from its inception several decades ago almost in parallel with the advances in biology, so much so that the latter is often considered to be almost exclusively an empirical…
Software now lies at the heart of scholarly research. Here we argue that as well as being important from a methodological perspective, software should, in many instances, be recognised as an output of research, equivalent to an academic…
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…