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Recommendations for the packaging and containerizing of bioinformatics software
11 references·8 citing·36 second hop
Recommendations for the packaging and containerizing of bioinformatics software (2018)Recommendations for the packaging and con…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The Galaxy platform for acces…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…Singularity: Scientific containers for mobility of compute (2017)Singularity: Scientific conta…Four simple recommendations to encourage best practices in research software (2017)Four simple recommendations t…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…Ten Simple Rules for Taking Advantage of Git and GitHub (2016)Ten Simple Rules for Taking A…1,500 scientists lift the lid on reproducibility (2016)1,500 scientists lift the lid…Tools and data services registry: a community effort to document bioinformatics resources (2015)Tools and data services regis…An introduction to Docker for reproducible research (2015)An introduction to Docker for…On best practices in the development of bioinformatics software (2014)On best practices in the deve…Ten Simple Rules for Reproducible Computational Research (2013)Ten Simple Rules for Reproduc…A multi-omics data analysis workflow packaged as a FAIR Digital Object (2024)A multi-omics data analysis w…Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability (2023)Meta-analysis of (single-cell…The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols (2021)The Dockstore: enhancing a co…Simplifying the development of portable, scalable, and reproducible workflows (2021)Simplifying the development o…Bioimage analysis workflows: community resources to navigate through a complex ecosystem (2021)Bioimage analysis workflows: …BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers (2021)BioContainers Registry: Searc…Software engineering for scientific big data analysis (2019)Software engineering for scie…Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software (2019)Bionitio: demonstrating and f…Reproducible Research in Computational Science (2011)Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation (2016)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)Automated assessment of psychiatric disorders using speech: A systematic review (2020)Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Galaxy: A platform for interactive large-scale genome analysis (2005)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Reproducibility in Science (2014)Good enough practices in scientific computing. (2017)Preferred reporting items for systematic reviews and meta‐analyses in ecology and evolutionary biology: a PRISMA extension (2021)Bioconductor: open software development for computational biology and bioinformatics (2004)BioCatalogue: a universal catalogue of web services for the life sciences (2010)BioMart: driving a paradigm change in biological data management (2011)Ten simple rules for making research software more robust (2017)The bio.tools registry of software tools and data resources for the life sciences (2019)WaveLab and Reproducible Research (1995)Git can facilitate greater reproducibility and increased transparency in science (2013)Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks (2019)Heterogeneous green innovations and carbon emission performance: Evidence at China's city level (2021)The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Towards FAIR principles for research software (2019)Towards reproducible computational drug discovery (2020)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Best Practices for Scientific Computing (2014)Promoting an open research culture (2015)How open science helps researchers succeed (2016)Ciw: An open-source discrete event simulation library (2018)Challenges and recommendations to improve the installability and archival stability of omics computational tools (2019)A large-scale study on research code quality and execution (2022)Snakemake—a scalable bioinformatics workflow engine (2012)A manifesto for reproducible science (2017)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)The nf-core framework for community-curated bioinformatics pipelines (2020)Sustainable data analysis with Snakemake (2021)Sustainable data analysis with Snakemake (2021)
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References

  • 20161,500 scientists lift the lid on reproducibility4,200 cited
  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2017Singularity: Scientific containers for mobility of compute2,734 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2015An introduction to Docker for reproducible research1,058 cited
  • 2013Ten Simple Rules for Reproducible Computational Research875 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2016Ten Simple Rules for Taking Advantage of Git and GitHub231 cited
  • 2015Tools and data services registry: a community effort to document bioinformatics resources153 cited
  • 2017Four simple recommendations to encourage best practices in research software140 cited
  • 2014On best practices in the development of bioinformatics software62 cited

Cited by

  • 2021The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols34 cited
  • 2021BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers31 cited
  • 2019Software engineering for scientific big data analysis

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29 cited
  • 2021Bioimage analysis workflows: community resources to navigate through a complex ecosystem22 cited
  • 2019Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software20 cited
  • 2023Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability17 cited
  • 2024A multi-omics data analysis workflow packaged as a FAIR Digital Object14 cited
  • 2021Simplifying the development of portable, scalable, and reproducible workflows12 cited