Related papers: Twelve years of SAMtools and BCFtools
Software Bills of Materials (SBOMs) have emerged as tools to facilitate the management of software dependencies, vulnerabilities, licenses, and the supply chain. While significant effort has been devoted to increasing SBOM awareness and…
The transfer learning toolkit wraps the codes of 17 transfer learning models and provides integrated interfaces, allowing users to use those models by calling a simple function. It is easy for primary researchers to use this toolkit and to…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Mutational signatures connect characteristic mutational patterns in the genome with biological or chemical processes that take place in cancers. Analysis of mutational signatures can help elucidate tumor evolution, prognosis, and…
R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
For agentic systems to use external tools to solve complex, long-horizon tasks, we need a large set of diverse and controllable tool-use environments. We introduce SynthTools, a fully LLM-based pipeline spanning the entire lifecycle:…
Large language models (LLMs) have recently achieved human-level performance on a range of professional and academic benchmarks. The accessibility of these models has lagged behind their performance. State-of-the-art LLMs require costly…
Frontier Large language models (LLMs) like ChatGPT and Gemini can decipher cryptic compiler errors for novice programmers, but their computational scale, cost, and tendency to over-assist make them problematic for widespread pedagogical…
As large language models (LLMs) like OpenAI's GPT series continue to make strides, we witness the emergence of artificial intelligence applications in an ever-expanding range of fields. In medicine, these LLMs hold considerable promise for…
TOPCAT is a desktop application for interactive analysis of tabular data, especially source catalogues. Along with its command-line counterpart STILTS, it has been under more or less continuous development for the past 15 years and is now…
The field of gamma-ray astronomy has seen important progress during the last decade, yet there exists so far no common software framework for the scientific analysis of gamma-ray telescope data. We propose to fill this gap by means of the…
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present…
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…
Single-cell analysis is an increasingly relevant approach in "omics'' studies. In the last decade, it has been applied to various fields, including cancer biology, neuroscience, and, especially, developmental biology. This rise in…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Apache SAMOA (Scalable Advanced Massive Online Analysis) is an open-source platform for mining big data streams. Big data is defined as datasets whose size is beyond the ability of typical software tools to capture, store, manage, and…