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Active matter systems, from self-propelled colloids to motile bacteria, are characterized by the conversion of free energy into useful work at the microscopic scale. They involve physics beyond the reach of equilibrium statistical…
High-dimensional longitudinal data is increasingly used in a wide range of scientific studies. To properly account for dependence between longitudinal observations, statistical methods for high-dimensional linear mixed models (LMMs) have…
In several industrial applications, such as crystallization, pollution control, and flow assurance, an accurate understanding of the aqueous electrolyte solutions is crucial. Electrolyte equilibrium calculation contributes with the design…
SfePy (Simple finite elements in Python) is a software for solving various kinds of problems described by partial differential equations in one, two or three spatial dimensions by the finite element method. Its source code is mostly (85\%)…
We present the package for the simulation of DM (Dark Matter) particles in fixed target experiments. The most convenient way of this simulation (and the only possible way in the case of beam-dump) is to simulate it in the framework of the…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Antimicrobial resistance (AMR) poses a global health threat, reducing the effectiveness of antibiotics and complicating clinical decision-making. To address this challenge, we introduce abx_amr_simulator, a Python-based simulation package…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
Abdominal aortic aneurysms (AAAs) are localized dilatations of the abdominal aorta that can lead to life-threatening rupture if left untreated. AAAs primarily affect older individuals, with high mortality rates following rupture, so early…
Agent based modelling is a computational approach that aims to understand the behaviour of complex systems through simplified interactions of programmable objects in computer memory called agents. Agent based models (ABMs) are predominantly…
mlpy is a Python Open Source Machine Learning library built on top of NumPy/SciPy and the GNU Scientific Libraries. mlpy provides a wide range of state-of-the-art machine learning methods for supervised and unsupervised problems and it is…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
PESummary is a Python software package for processing and visualising data from any parameter estimation code. The easy to use Python executable scripts and extensive online documentation has resulted in PESummary becoming a key component…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
A statistical emulator can be used as a surrogate of complex physics-based calculations to drastically reduce the computational cost. Its successful implementation hinges on an accurate representation of the nonlinear response surface with…
Data analysis in fundamental sciences nowadays is an essential process that pushes frontiers of our knowledge and leads to new discoveries. At the same time we can see that complexity of those analyses increases fast due to a)~enormous…
Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…
imbalanced-ensemble, abbreviated as imbens, is an open-source Python toolbox for leveraging the power of ensemble learning to address the class imbalance problem. It provides standard implementations of popular ensemble imbalanced learning…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
A working group on detector simulation was formed as part of the high-energy physics (HEP) Software Foundation's initiative to prepare a Community White Paper that describes the main software challenges and opportunities to be faced in the…