Related papers: linemake: An Atomic and Molecular Line List Genera…

Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…

Molecular line lists are important for modelling absorption and emission processes in atmospheres of different astronomical objects, such as cool stars and exoplanets. In order to be applicable for high temperatures, line lists for…

The ExoMol database aims to provide comprehensive molecular line lists for exoplanetary and other hot atmospheres. The data are expanded by inclusion of empirically derived line lists taken from the literature for a series of diatomic…

Transforming dense, detailed, unstructured text into an interpretable and summarised table, also colloquially known as Text-to-Table generation, is an essential task for information retrieval. Current methods, however, miss out on how and…

Evaluating outputs of large language models (LLMs) is challenging, requiring making -- and making sense of -- many responses. Yet tools that go beyond basic prompting tend to require knowledge of programming APIs, focus on narrow domains,…

Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…

Generative models for molecules have shown considerable promise for use in computational chemistry, but remain difficult to use for non-experts. For this reason, we introduce open-source infrastructure for easily building generative…

Atomic and molecular data for the transitions of a number of astrophysically interesting species are summarized, including energy levels, statistical weights, Einstein A-coefficients and collisional rate coefficients. Available collisional…

We describe a real-time system that receives a live audio stream from a jam session and generates lyric lines that are congruent with the live music being played. Two novel approaches are proposed to align the learned latent spaces of audio…

In this article we report the release of a new program for calculating the emissivity of atomic transitions. The program, which can be obtained with its documentation from our website www.scienceware.net, passed various rigorous tests and…

Machine Learning (ML) is increasingly used to automate impactful decisions, which leads to concerns regarding their correctness, reliability, and fairness. We envision highly-automated software platforms to assist data scientists with…

Spectral line observations are an indispensable tool to remotely probe the physical and chemical conditions throughout the universe. Modelling their behaviour is a computational challenge that requires dedicated software. In this paper, we…

Atomistic structural data are central to materials science, condensed matter physics, and chemistry, and are increasingly digitised across diverse repositories and databases. Interoperable access to these heterogeneous data sources enables…

We describe the creation of a new Atomic and Molecular Physics science gateway (AMPGateway). The gateway is designed to bring together a subset of the AMP community to work collectively to make their codes available and easier to use by the…

We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…

In this paper we describe the conception of a software toolkit designed for the construction, maintenance and collaborative use of a Generative Lexicon. In order to ease its portability and spreading use, this tool was built with free and…

Generative machine learning models for exploring chemical space have shown immense promise, but many molecules they generate are too difficult to synthesize, making them impractical for further investigation or development. In this work, we…

Empirical research on code review processes is increasingly central to understanding software quality and collaboration. However, collecting and analyzing review data remains a time-consuming and technically intensive task. Most researchers…

Over the past few decades, a vast amount of information on the structure of atomic nuclei has been collected, compiled, and evaluated. Accurate and reliable data are essential for the understanding of the behavior of atomic nuclei.…

The development of synthesis procedures remains a fundamental challenge in materials discovery, with procedural knowledge scattered across decades of scientific literature in unstructured formats that are challenging for systematic…