Special issue on software citation, indexing, and discoverability.

Software plays a fundamental role in research as a tool, an output, or even as an object of study. This special issue on software citation, indexing, and discoverability brings together five papers examining different aspects of how the use of software is recorded and made available to others. It describes new work on datasets that enable large-scale analysis of the evolution of software usage and citation, that presents evidence of increased citation rates when software artifacts are released, that provides guidance for registries and repositories to support software citation and findability, and that shows there are still barriers to improving and formalising software citation and publication practice.

Introducing the FAIR Principles for research software.

Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value.

The conservation of human functional variants and their effects across livestock species.

Despite the clear potential of livestock models of human functional variants to provide important insights into the biological mechanisms driving human diseases and traits, their use to date has been limited. Generating such models via genome editing is costly and time consuming, and it is unclear which variants will have conserved effects across species. In this study we address these issues by studying naturally occurring livestock models of human functional variants.

Recognizing the value of software: a software citation guide.

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience.

hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets.

Understanding how the genome is shaped by selective processes forms an integral part of modern biology. However, as genomic datasets continue to grow larger it is becoming increasingly difficult to apply traditional statistics for detecting signatures of selection to these cohorts. There is therefore a pressing need for the development of the next generation of computational and analytical tools for detecting signatures of selection in large genomic datasets.

Best practices for scientific computing.

We describe a set of best practices for scientific software development, based on research and experience, that will improve scientists' productivity and the reliability of their software.