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BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
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BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations (2022)BioExcel Building Blocks Workflows (BioBB…Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory (2021)Implementing FAIR Digital Obj…Towards FAIR principles for research software (2019)Towards FAIR principles for r…Surviving the deluge of biosimulation data (2019)Surviving the deluge of biosi…BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows (2019)BioExcel Building Blocks, a s…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…Positioning and Power in Academic Publishing: Players, Agents and Agendas (2016)Positioning and Power in Acad…Tools and data services registry: a community effort to document bioinformatics resources (2015)Tools and data services regis…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…Design Patterns: Elements of Reusable Object-Oriented Software (1994)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)Four simple recommendations to encourage best practices in research software (2017)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)Galaxy: A platform for interactive large-scale genome analysis (2005)What does research reproducibility mean? (2016)The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)Towards reproducible computational drug discovery (2020)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Snakemake—a scalable bioinformatics workflow engine (2012)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)The nf-core framework for community-curated bioinformatics pipelines (2020)Sustainable data analysis with Snakemake (2021)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)Nextflow enables reproducible computational workflows (2017)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Simulation Foundry: Automated and F.A.I.R. Molecular Modeling (2020)Supercomputing with MPI meets the Common Workflow Language standards: an experience report (2020)Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations (2024)Programmatic access to bioinformatics tools from EMBL-EBI update: 2017 (2017)Sharing Data from Molecular Simulations (2019)The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019)A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort (2023)KBase: The United States Department of Energy Systems Biology Knowledgebase (2018)Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (2019)Topic Modeling in Management Research: Rendering New Theory from Textual Data (2019)Bayesian Analysis Reporting Guidelines (2021)A large-scale study on research code quality and execution (2022)Ten quick tips for building FAIR workflows (2023)Recording provenance of workflow runs with RO-Crate (2024)WorkflowHub: a registry for computational workflows (2025)
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References

  • 2010Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences3,455 cited
  • 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update2,149 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2016Positioning and Power in Academic Publishing: Players, Agents and Agendas935 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2019Towards FAIR principles for research software322 cited
  • 2015Tools and data services registry: a community effort to document bioinformatics resources153 cited
  • 2019BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows85 cited
  • 2021Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory70 cited
  • 2019Surviving the deluge of biosimulation data45 cited

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