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Improving the usability and archival stability of bioinformatics software
3 references·8 citing·39 second hop
Improving the usability and archival stability of bioinformatics software (2019)Improving the usability and archival stab…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…Ten Simple Rules for Developing Usable Software in Computational Biology (2017)Ten Simple Rules for Developi…Reproducibility of computational workflows is automated using continuous analysis (2017)Reproducibility of computatio…How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools (2026)How to make big data accessib…Packaging and containerization of computational methods (2024)Packaging and containerizatio…Improving bioinformatics software quality through incorporation of software engineering practices (2022)Improving bioinformatics soft…Principles of resilient coding for plant ecophysiologists (2021)Principles of resilient codin…Fostering reproducibility, reusability, and technology transfer in health informatics (2021)Fostering reproducibility, re…A Practical Guide to Metabolomics Software Development (2021)A Practical Guide to Metabolo…iMicrobe: Tools and data-driven discovery platform for the microbiome sciences (2019)iMicrobe: Tools and data-driv…Essential guidelines for computational method benchmarking (2019)Essential guidelines for comp…Galaxy: A platform for interactive large-scale genome analysis (2005)Snakemake—a scalable bioinformatics workflow engine (2012)Ten Simple Rules for Reproducible Computational Research (2013)Ten simple rules for documenting scientific software (2018)Ten simple rules on writing clean and reliable open-source scientific software (2021)Reproducible Research in Computational Science (2011)An introduction to Docker for reproducible research (2015)1,500 scientists lift the lid on reproducibility (2016)Challenges and recommendations to improve the installability and archival stability of omics computational tools (2019)The Kipoi repository accelerates community exchange and reuse of predictive models for genomics (2019)The five pillars of computational reproducibility: bioinformatics and beyond (2023)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)Why Most Published Research Findings Are False (2005)Why Most Published Research Findings Are False (2005)Reproducible and replicable comparisons using SummarizedBenchmark (2018)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)BioContainers: an open-source and community-driven framework for software standardization (2017)Singularity: Scientific containers for mobility of compute (2017)KBase: The United States Department of Energy Systems Biology Knowledgebase (2018)Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue (2022)Git can facilitate greater reproducibility and increased transparency in science (2013)PhenoMeNal: processing and analysis of metabolomics data in the cloud (2018)MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools (2021)Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study (2024)The Impact of Public R&D Expenditure on Business R&D (2000)The impact of public R&D expenditure on business R&D (2000)The Eu General Data Protection Regulation (Gdpr): A Practical Guide (2017)A nested model for AI design and validation (2024)Ten Simple Rules for the Open Development of Scientific Software (2012)Best Practices for Scientific Computing (2014)Bioconductor: open software development for computational biology and bioinformatics (2004)Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)Nextflow enables reproducible computational workflows (2017)Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics (2024)A how-to guide for code sharing in biology (2024)Autonomous Self‐Evolving Research on Biomedical Data: The DREAM Paradigm (2025)
this work references cited by second hop

References

  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2017Reproducibility of computational workflows is automated using continuous analysis151 cited
  • 2017Ten Simple Rules for Developing Usable Software in Computational Biology84 cited

Cited by

  • 2021A Practical Guide to Metabolomics Software Development56 cited
  • 2021Principles of resilient coding for plant ecophysiologists39 cited
  • 2019iMicrobe: Tools and data-driven discovery platform for the microbiome sciences28 cited
  • 2024Packaging and containerization of computational methods24 cited
  • 2019Essential guidelines for computational method benchmarking21 cited
  • 2022Improving bioinformatics software quality through incorporation of software engineering practices17 cited
  • 2021Fostering reproducibility, reusability, and technology transfer in health informatics11 cited
  • 2026How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools10 cited

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