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Ruffus: a lightweight Python library for computational pipelines
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Ruffus: a lightweight Python library for computational pipelines (2010)Ruffus: a lightweight Python library for …Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Taverna: a tool for the compo…Ten simple rules and a template for creating workflows-as-applications (2022)Ten simple rules and a templa…CGAT-core: a python framework for building scalable, reproducible computational biology workflows (2019)CGAT-core: a python framework…Anduril 2: upgraded large-scale data integration framework (2019)Anduril 2: upgraded large-sca…TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses (2018)TOGGLe, a flexible framework …Ten Simple Rules for Developing Usable Software in Computational Biology (2017)Ten Simple Rules for Developi…Jug: Software for Parallel Reproducible Computation in Python (2017)Jug: Software for Parallel Re…Investigating reproducibility and tracking provenance – A genomic workflow case study (2017)Investigating reproducibility…Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles (2016)Towards agile large-scale pre…Planning bioinformatics workflows using an expert system (2016)Planning bioinformatics workf…FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures (2016)FabSim: Facilitating computat…Omics Pipe: a community-based framework for reproducible multi-omics data analysis (2015)Omics Pipe: a community-based…Experiences with workflows for automating data-intensive bioinformatics (2015)Experiences with workflows fo…β-catenin mediates stress resilience through Dicer1/microRNA regulation (2014)β-catenin mediates stress res…iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations (2014)iPortal: the swiss grid prote…BigDataScript: a scripting language for data pipelines (2014)BigDataScript: a scripting la…Conveyor: a workflow engine for bioinformatic analyses (2011)Conveyor: a workflow engine f…The Science of Resilience: Implications for the Prevention and Treatment of Depression (2012)DICER1 and microRNA regulation in post-traumatic stress disorder with comorbid depression (2015)Germ Cell Origins of Posttraumatic Stress Disorder Risk: The Transgenerational Impact of Parental Stress Experience (2015)Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder (2017)Kepler: An Extensible System for Design and Execution of Scientific Workflows (2004)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)Bioinformatic pipelines in Python with Leaf (2013)Parallelization in Scientific Workflow Management Systems (2013)NeatSeq-Flow: A Lightweight High-Throughput Sequencing Workflow Platform for Non-Programmers and Programmers Alike (2017)Snakemake—a scalable bioinformatics workflow engine (2012)The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions (2016)Isabl Platform, a digital biobank for processing multimodal patient data (2020)Galaxy: A platform for interactive large-scale genome analysis (2005)KNIME - the Konstanz information miner (2009)openBIS: a flexible framework for managing and analyzing complex data in biology research (2011)qPortal: A platform for data-driven biomedical research (2018)Ten Simple Rules for Reproducible Computational Research (2013)Ten simple rules for documenting scientific software (2018)Improving the usability and archival stability of bioinformatics software (2019)A Practical Guide to Metabolomics Software Development (2021)1,500 scientists lift the lid on reproducibility (2016)Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines (2018)Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines (2019)Applying the FAIR Principles to computational workflows (2025)Nextflow enables reproducible computational workflows (2017)An Empirical Investigation on the Challenges in Scientific Workflow Systems Development (2025)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Workflows and e-Science: An overview of workflow system features and capabilities (2008)SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines (2019)Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems (2023)
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References

  • 2004Taverna: a tool for the composition and enactment of bioinformatics workflows1,602 cited

Cited by

  • 2014β-catenin mediates stress resilience through Dicer1/microRNA regulation240 cited
  • 2017Ten Simple Rules for Developing Usable Software in Computational Biology84 cited
  • 2017Investigating reproducibility and tracking provenance – A genomic workflow case study76 cited
  • 2015Omics Pipe: a community-based framework for reproducible multi-omics data analysis75 cited
  • 2015Experiences with workflows for automating data-intensive bioinformatics64 cited
  • 2019CGAT-core: a python framework for building scalable, reproducible computational biology workflows50 cited
  • 2014iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations43 cited
  • 2019Anduril 2: upgraded large-scale data integration framework43 cited
  • 2011Conveyor: a workflow engine for bioinformatic analyses39 cited
  • 2017Jug: Software for Parallel Reproducible Computation in Python39 cited
  • 2016FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures38 cited
  • 2016Planning bioinformatics workflows using an expert system38 cited
  • 2014BigDataScript: a scripting language for data pipelines

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34 cited
  • 2016Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles33 cited
  • 2022Ten simple rules and a template for creating workflows-as-applications24 cited
  • 2018TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses24 cited