ArticleBioinformatics (Oxford, England)2024
FAIRsoft-a practical implementation of FAIR principles for research software.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
- PDBe-SIFTS: An open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.Protein science : a publication of the Protein Society · 2026Article
- Do papers tell the whole story? A benchmark and framework for uncovering hidden implementation gaps in bioinformatics.Briefings in bioinformatics · 2026Article
- bio.tools: an expanded web service for research software in the life sciences.Nucleic acids research · 2026Article
- PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.bioRxiv : the preprint server for biology · 2026Article
- Federated learning frameworks: quality and interoperability for biomedical research.NAR genomics and bioinformatics · 2026Review
- Software engineering for reproducible pipeline development in bioinformatics.Frontiers in bioinformatics · 2026Review
- WorkflowHub: a registry for computational workflows.Scientific data · 2025Article
- A study on interoperability between two Personal Health Train infrastructures in leukodystrophy data analysis.Scientific data · 2024Article
- Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.PLoS computational biology · 2024Article
- A multi-omics data analysis workflow packaged as a FAIR Digital Object.GigaScience · 2024Article
- From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure.F1000Research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
motivationSoftware plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce and verify. It could be undocumented, opaque, contain unknown errors that affect the outcome, or be directly unavailable and impossible to use for others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software in the domain should meet to ensure its quality and sustainability, resembling the FAIR (findable, accessible, interoperable, and reusable) data principles.
resultsWe present here a comprehensive series of quantitative indicators based on a pragmatic interpretation of the FAIR Principles and their implementation on OpenEBench, ELIXIR's open platform providing both support for scientific benchmarking and an active observatory of quality-related features for Life Sciences research software. The results serve to understand the current practices around research software quality-related features and provide objective indications for improving them. AVAILABILITY AND IMPLEMENTATION: Software metadata, from 11 different sources, collected, integrated, and analysed in the context of this manuscript are available at https://doi.org/10.5281/zenodo.7311067. Code used for software metadata retrieval and processing is available in the following repository: https://gitlab.bsc.es/inb/elixir/software-observatory/FAIRsoft_ETL.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.