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Managing data and code in open scientific research is complicated by two key problems: large datasets often cannot be stored alongside code in repository platforms like GitHub, and iterative analysis can lead to unnoticed changes to data,…
Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII,…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
The Software Bill of Materials (SBOM) has emerged as a promising solution, providing a machine-readable inventory of software components used, thus bolstering supply chain security. This paper presents an extensive study concerning the…
Even though numerous researchers require stable datasets along with source code and basic metrics calculated on them, neither GitHub nor any other code hosting platform provides such a resource. Consequently, each researcher must download…
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA…
Recently, tool learning with large language models (LLMs) has emerged as a promising paradigm for augmenting the capabilities of LLMs to tackle highly complex problems. Despite growing attention and rapid advancements in this field, the…
Purpose. The increasing emphasis on data quantity in research infrastructures has highlighted the need for equally robust mechanisms ensuring data quality, particularly in bibliographic and citation datasets. This paper addresses the…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing…
In year 2006 Bio-Linux with the work of Tim Booth and team gives its rising and provide an operating system that was and still specialized in providing a bioinformatic specific software environment for the working needs in this corner of…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
Context: When software is released publicly, it is common to include with it either the full text of the license or licenses under which it is published, or a detailed reference to them. Therefore public licenses, including FOSS (free, open…
Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However,…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…
In software development there is a constant pressure to produce code faster and faster without compromising on quality. New tools supporting developers are created in response to this demand. Currently a new generation of such solutions is…
This manual describes a set of utilities developed for Lattice QCD computations. They are collectively called QCDUtils. They comprise a set of Python programs each of them with a specific function: download gauge ensembles from the public…
Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the…
Integrating Artificial Intelligence into Software Engineering (SE) requires having a curated collection of models suited to SE tasks. With millions of models hosted on Hugging Face (HF) and new ones continuously being created, it is…