Related papers: Twelve years of SAMtools and BCFtools
Scientific software is one of the key elements for reproducible research. However, classic publications and related scientific software are typically not (sufficiently) linked, and it lacks tools to jointly explore these artefacts. In this…
We present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
The software development lifecycle depends heavily on the testing process, which is an essential part of finding issues and reviewing the quality of software. Software testing can be done in two ways: manually and automatically. With an…
With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
The structural identifiability and the observability of a model determine the possibility of inferring its parameters and states by observing its outputs. These properties should be analysed before attempting to calibrate a model.…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
With the exponential growth of the life science literature, biomedical text mining (BTM) has become an essential technology for accelerating the extraction of insights from publications. Identifying named entities (e.g., diseases, drugs, or…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
As computer systems become more and more complex, software and tools lag more and more behind. This is especially true for scientific software that often demands high performance, and thus needs to take advantage of parallelisms, memory…
PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows.…
Modern software applications heavily rely on diverse third-party components, libraries, and frameworks sourced from various vendors and open source repositories, presenting a complex challenge for securing the software supply chain. To…
Large language models (LLMs) are typically trained on enormous quantities of unlicensed text, a practice that has led to scrutiny due to possible intellectual property infringement and ethical concerns. Training LLMs on openly licensed text…
DevOps is a combination of methodologies and tools that improves the software development, build, deployment, and monitoring processes by shortening its lifecycle and improving software quality. Part of this process is CI/CD, which embodies…
Two years on from the initial release of AlphaFold2 we have seen its widespread adoption as a structure prediction tool. Here we discuss some of the latest work based on AlphaFold2, with a particular focus on its use within the structural…
Over the last few years, with the growth of time-series collecting and storing, there has been a great demand for tools and software for temporal data engineering and modeling. This paper presents a generic workflow for time series data…
$\tt DsixTools$ is a Mathematica package for the handling of the Standard Model Effective Field Theory (SMEFT) and the Low-energy Effective Field Theory (LEFT) with operators up to dimension six, both at the algebraic and numerical level.…
We introduce a large-scale dataset of the complete texts of free/open source software (FOSS) license variants. To assemble it we have collected from the Software Heritage archive-the largest publicly available archive of FOSS source code…
Recently, DNA data storage systems have attracted many researchers worldwide. Motivated by the success stories of such systems, in this work we propose a software called BacSoft to clone the data in a bacterial plasmid by using the concept…