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Software engineering for scientific big data analysis
14 references·3 citing·36 second hop
Software engineering for scientific big data analysis (2019)Software engineering for scientific big d…Recommendations for the packaging and containerizing of bioinformatics software (2019)Recommendations for the packa…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The Galaxy platform for acces…Recommendations for the packaging and containerizing of bioinformatics software (2018)Recommendations for the packa…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…Ten simple rules for making research software more robust (2017)Ten simple rules for making r…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…Tools and techniques for computational reproducibility (2016)Tools and techniques for comp…Ten Simple Rules for Taking Advantage of Git and GitHub (2016)Ten Simple Rules for Taking A…Best Practices for Scientific Computing (2014)Best Practices for Scientific…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…Ten Simple Rules for Reproducible Computational Research (2013)Ten Simple Rules for Reproduc…Ten Simple Rules for the Open Development of Scientific Software (2012)Ten Simple Rules for the Open…Snakemake—a scalable bioinformatics workflow engine (2012)Snakemake—a scalable bioinfor…Bpipe: a tool for running and managing bioinformatics pipelines (2012)Bpipe: a tool for running and…Global quantitative analysis and visualization of big data and medical devices based on bibliometrics (2024)Global quantitative analysis …A multi-omics data analysis workflow packaged as a FAIR Digital Object (2024)A multi-omics data analysis w…Ten simple rules for making a software tool workflow-ready (2022)Ten simple rules for making a…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)AiiDA: automated interactive infrastructure and database for computational science (2015)A review of bioinformatic pipeline frameworks (2016)BioContainers: an open-source and community-driven framework for software standardization (2017)Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Galaxy: A platform for interactive large-scale genome analysis (2005)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)WaveLab and Reproducible Research (1995)Git can facilitate greater reproducibility and increased transparency in science (2013)Four simple recommendations to encourage best practices in research software (2017)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)Reproducibility: A tragedy of errors (2016)The nf-core framework for community-curated bioinformatics pipelines (2020)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Singularity: Scientific containers for mobility of compute (2017)Sustainable data analysis with Snakemake (2021)Design of Experiments (1936)The Logic of Scientific Discovery. (1959)Design and Analysis of Computer Experiments (1989)Reproducible and replicable pain research: a critical review (2018)Recommendations to enhance rigor and reproducibility in biomedical research (2020)EntropyHub: An open-source toolkit for entropic time series analysis (2021)SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis (2016)Investigating reproducibility and tracking provenance – A genomic workflow case study (2017)Playing Super Mario 64 increases hippocampal grey matter in older adults (2017)Sustainable data analysis with Snakemake (2021)Our path to better science in less time using open data science tools (2017)A Large-Scale Study About Quality and Reproducibility of Jupyter Notebooks (2019)
this work references cited by second hop

References

  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2012Snakemake—a scalable bioinformatics workflow engine2,775 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2013Ten Simple Rules for Reproducible Computational Research875 cited
  • 2014Best Practices for Scientific Computing715 cited
  • 2013The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud678 cited
  • 2016Ten Simple Rules for Taking Advantage of Git and GitHub231 cited
  • 2016Tools and techniques for computational reproducibility169 cited
  • 2012Bpipe: a tool for running and managing bioinformatics pipelines159 cited
  • 2012Ten Simple Rules for the Open Development of Scientific Software143 cited
  • 2017Ten simple rules for making research software more robust111 cited
  • 2019Recommendations for the packaging and containerizing of bioinformatics software50 cited
  • 2018Recommendations for the packaging and containerizing of bioinformatics software38 cited

Cited by

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2022
Ten simple rules for making a software tool workflow-ready
18 cited
  • 2024Global quantitative analysis and visualization of big data and medical devices based on bibliometrics15 cited
  • 2024A multi-omics data analysis workflow packaged as a FAIR Digital Object14 cited