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The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS)…
Optimization techniques play an important role in several scientific and real-world applications, thus becoming of great interest for the community. As a consequence, a number of open-source libraries are available in the literature, which…
In this paper we present Simgrid, a toolkit for the versatile simulation of large scale distributed systems, whose development effort has been sustained for the last fifteen years. Over this time period SimGrid has evolved from a…
Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the…
The library scikit-fda is a Python package for Functional Data Analysis (FDA). It provides a comprehensive set of tools for representation, preprocessing, and exploratory analysis of functional data. The library is built upon and integrated…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Recent advancements in generative machine learning have enabled rapid progress in biological design tools (BDTs) such as protein structure and sequence prediction models. The unprecedented predictive accuracy and novel design capabilities…
Biomolecular computers, along with quantum computers, may be a future alternative for traditional, silicon-based computers. Main advantages of biomolecular computers are massive parallel processing of data, expanded capacity of storing…
Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often created de novo, based on reading the literature and…
A Software Bill of Materials (SBOM) is a machine-readable artifact that systematically organizes software information, enhancing supply chain transparency and security. To facilitate the exchange and utilization of SBOMs, organizations such…
A Software Bill of Materials (SBOM) provides transparency by documenting software component metadata and dependencies. However, SBOM adoption depends on tool ecosystems. With two dominant formats: SPDX and CycloneDX - the ecosystems vary…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
This paper presents Deepchecks, a Python library for comprehensively validating machine learning models and data. Our goal is to provide an easy-to-use library comprising of many checks related to various types of issues, such as model…
SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…
GitHub hosts hundreds of millions of code repositories written in hundreds of different programming languages. In addition to its hosting services, GitHub provides data and insights into code, such as vulnerability analysis and code…
Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…