Related papers: Development & Implementation of a PyMOL 'putty' Re…
Multiple Instance Learning (MIL) gains popularity in many real-life machine learning applications due to its weakly supervised nature. However, the corresponding effort on explaining MIL lags behind, and it is usually limited to presenting…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
Research into the processes of photoionised nebulae plays a significant part in our understanding of stellar evolution. It is extremely difficult to visually represent or model ionised nebula, requiring astronomers to employ sophisticated…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…
We present PrismSSL, a Python library that unifies state-of-the-art self-supervised learning (SSL) methods across audio, vision, graphs, and cross-modal settings in a single, modular codebase. The goal of the demo is to show how researchers…
We introduce geoplotlib, an open-source python toolbox for visualizing geographical data. geoplotlib supports the development of hardware-accelerated interactive visualizations in pure python, and provides implementations of dot maps,…
Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…
Graphical user interface (GUI) has become integral to modern society, making it crucial to be understood for human-centric systems. However, unlike natural images or documents, GUIs comprise artificially designed graphical elements arranged…
We present a new program able to perform visual structural analysis on 3D particle systems called PASYVAT (PArticle SYstem Visual Analysis Tool). More specifically, it can select multiple interparticle distance ranges from a radial…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
POLEVAL provides a software toolbox for collaborative, persistent and reproducible analysis of XPS experiments. It allows to treat, analyse and visualise the results of an extended experimental campaign in a single python notebook in a…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
Small and wide angle x-ray scattering tensor tomography are powerful methods for studying anisotropic nanostructures in a volume-resolved manner, and are becoming increasingly available to users of synchrotron facilities. The analysis of…
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular…
Multimodal approaches that integrate histology and genomics hold strong potential for precision oncology. However, phenotypic and genotypic heterogeneity limits the quality of intra-modal representations and hinders effective inter-modal…
PyUltraLight simulates the dynamics of ultralight dark matter in a non-expanding background. PyUltraLight can describe the evolution of several interacting ultralight dark matter halos or one or more halos orbiting a central, fixed…