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Using bio.tools to generate and annotate workbench tool descriptions
16 references·0 citing·28 second hop
Using bio.tools to generate and annotate workbench tool descriptions (2017)Using bio.tools to generate and annotate …Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows (2017)The Dockstore: enabling modul…Practical Computational Reproducibility in the Life Sciences (2017)Practical Computational Repro…General guidelines for biomedical software development (2017)General guidelines for biomed…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…A public Galaxy platform at Pasteur used as an execution engine for web services (2017)A public Galaxy platform at P…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…Common Workflow Language, draft 3 (2016)Common Workflow Language, dra…Tools and data services registry: a community effort to document bioinformatics resources (2015)Tools and data services regis…BioShaDock: a community driven bioinformatics shared Docker-based tools registry (2015)BioShaDock: a community drive…The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)The Taverna workflow suite: d…Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists (2010)Galaxy: A Web‐Based Genome An…Community-driven computational biology with Debian Linux (2010)Community-driven computationa…BioCatalogue: a universal catalogue of web services for the life sciences (2010)BioCatalogue: a universal cat…Galaxy: A platform for interactive large-scale genome analysis (2005)Galaxy: A platform for intera…Using Galaxy to Perform Large‐Scale Interactive Data Analyses (2007)Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline (2014)Taverna: a tool for building and running workflows of services (2006)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)myExperiment: a repository and social network for the sharing of bioinformatics workflows (2010)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Bioconductor: open software development for computational biology and bioinformatics (2004)BioMart: driving a paradigm change in biological data management (2011)The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019)The nf-core framework for community-curated bioinformatics pipelines (2020)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)BioMOBY: An open source biological web services proposal (2002)Kepler: An Extensible System for Design and Execution of Scientific Workflows (2004)Analysis Tool Web Services from the EMBL-EBI (2013)Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users (2021)The biology workbench—A seamless database and analysis environment for the biologist (1998)ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources (2001)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022)Does Gamification Work? -- A Literature Review of Empirical Studies on Gamification (2014)What does research reproducibility mean? (2016)Bioboxes: standardised containers for interchangeable bioinformatics software (2015)Snakemake—a scalable bioinformatics workflow engine (2012)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)Sustainable data analysis with Snakemake (2021)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (2019)
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References

  • 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update2,149 cited
  • 2005Galaxy: A platform for interactive large-scale genome analysis2,027 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2010Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists1,430 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2013The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud678 cited
  • 2010BioCatalogue: a universal catalogue of web services for the life sciences217 cited
  • 2016Common Workflow Language, draft 3212 cited
  • 2017Practical Computational Reproducibility in the Life Sciences171 cited
  • 2015Tools and data services registry: a community effort to document bioinformatics resources156 cited
  • 2017Four simple recommendations to encourage best practices in research software143 cited
  • 2017The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows83 cited
  • 2010Community-driven computational biology with Debian Linux68 cited
  • 2017A public Galaxy platform at Pasteur used as an execution engine for web services

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44 cited
  • 2015BioShaDock: a community driven bioinformatics shared Docker-based tools registry37 cited
  • 2017General guidelines for biomedical software development25 cited
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