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The bio.tools registry of software tools and data resources for the life sciences
3 references·16 citing·31 second hop
The bio.tools registry of software tools and data resources for the life sciences (2019)The bio.tools registry of software tools …The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The Galaxy platform for acces…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…Tools and data services registry: a community effort to document bioinformatics resources (2015)Tools and data services regis…WorkflowHub: a registry for computational workflows (2025)WorkflowHub: a registry for c…Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection (2024)Introduction of the Capsules …Bioinformatics software development: Principles and future directions (2024)Bioinformatics software devel…A qualitative assessment of using ChatGPT as large language model for scientific workflow development (2024)A qualitative assessment of u…Ten quick tips for building FAIR workflows (2023)Ten quick tips for building F…ELIXIR and Toxicology: a community in development (2023)ELIXIR and Toxicology: a comm…Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems (2023)Developing and reusing bioinf…Nine best practices for research software registries and repositories (2022)Nine best practices for resea…Improving bioinformatics software quality through incorporation of software engineering practices (2022)Improving bioinformatics soft…Galaxy: A Decade of Realising CWFR Concepts (2022)Galaxy: A Decade of Realising…Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology (2021)Practical resources for enhan…Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service (2021)Laniakea@ReCaS: exploring the…ELIXIR and Toxicology: a community in development (2021)ELIXIR and Toxicology: a comm…biotoolsSchema: a formalized schema for bioinformatics software description (2021)biotoolsSchema: a formalized …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…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)BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows (2019)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 reproducible computational drug discovery (2020)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Galaxy: A platform for interactive large-scale genome analysis (2005)Singularity: Scientific containers for mobility of compute (2017)Sustainable data analysis with Snakemake (2021)Towards FAIR principles for research software (2019)Perspectives on automated composition of workflows in the life sciences (2021)Snakemake—a scalable bioinformatics workflow engine (2012)Nextflow enables reproducible computational workflows (2017)Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments (2021)Accelerating bioinformatics implementation in public health (2023)The nf-core framework for community-curated bioinformatics pipelines (2020)Sustainable data analysis with Snakemake (2021)Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks (2022)Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice (2023)Collaboration gets the most out of software (2013)1,500 scientists lift the lid on reproducibility (2016)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)A terminology for scientific workflow systems (2025)Molecular biology in the exabyte era: Taming the data deluge for biological revelation and clinical transformation (2025)Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update (2026)Plan, Generate and Match: Scientific Workflow Recommendation with Large Language Models (2023)A python workflow definition for computational materials design (2025)
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References

  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2015Tools and data services registry: a community effort to document bioinformatics resources153 cited

Cited by

  • 2025WorkflowHub: a registry for computational workflows46 cited
  • 2023Ten quick tips for building FAIR workflows42 cited
  • 2023Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems41 cited
  • 2021BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers31 cited
  • 2024Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection24 cited
  • 2021Bioimage analysis workflows: community resources to navigate through a complex ecosystem22 cited
  • 2021biotoolsSchema: a formalized schema for bioinformatics software description20 cited
  • 2022Nine best practices for research software registries and repositories18 cited
  • 2022Improving bioinformatics software quality through incorporation of software engineering practices17 cited
  • 2024Bioinformatics software development: Principles and future directions17 cited
  • 2024

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A qualitative assessment of using ChatGPT as large language model for scientific workflow development
15 cited
  • 2021Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology14 cited
  • 2022Galaxy: A Decade of Realising CWFR Concepts12 cited
  • 2021Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service8 cited
  • 2021ELIXIR and Toxicology: a community in development7 cited
  • 2023ELIXIR and Toxicology: a community in development7 cited