ArticleGigaScience2015
Bioboxes: standardised containers for interchangeable bioinformatics software.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
42 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Packaging and containerization of computational methods.Nature protocols · 2024Pooled it
- Tissue specificity of in vitro drug sensitivity.Journal of the American Medical Informatics Association : JAMIA · 2018Pooled it
- Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.Nature biotechnology · 2026Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance.Emerging infectious diseases · 2025Article
- MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.Bioinformatics (Oxford, England) · 2024Article
- Challenges and opportunities in sharing microbiome data and analyses.Nature microbiology · 2023Review
- Improving bioinformatics software quality through incorporation of software engineering practices.PeerJ. Computer science · 2022Article
- Microbiome signature and diversity regulates the level of energy production under anaerobic condition.Scientific reports · 2021Article
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Article
- Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.Nature protocols · 2021Review
- A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing.F1000Research · 2021Article
- Incidence of Arterial Hypertension in People With Periodontitis and Characterization of the Oral and Subgingival Microbiome: A Study Protocol.Frontiers in cardiovascular medicine · 2021Article
- LEMMI: a continuous benchmarking platform for metagenomics classifiers.Genome research · 2020Article
- Towards reproducible computational drug discovery.Journal of cheminformatics · 2020Review
- CAMITAX: Taxon labels for microbial genomes.GigaScience · 2020Article
- Building Containerized Workflows Using the BioDepot-Workflow-Builder.Cell systems · 2019Article
- ORCA: a comprehensive bioinformatics container environment for education and research.Bioinformatics (Oxford, England) · 2019Article
- Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.GigaScience · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.
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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.