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Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
9 references·5 citing·32 second hop
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics (2018)Developing reproducible bioinformatics an…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…Common Workflow Language, draft 3 (2016)Common Workflow Language, dra…A review of bioinformatic pipeline frameworks (2016)A review of bioinformatic pip…Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses (2014)Cloud-based bioinformatics wo…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…Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support (2012)Tavaxy: Integrating Taverna a…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…H3AGWAS: a portable workflow for genome wide association studies (2022)H3AGWAS: a portable workflow …Using prototyping to choose a bioinformatics workflow management system (2021)Using prototyping to choose a…The H3Africa Consortium: Publication Outputs of a Pan-African Genomics Collaboration (2013 to 2020) (2021)The H3Africa Consortium: Publ…Publishing reproducible dynamic kinetic models (2020)Publishing reproducible dynam…Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience (2019)Organizing and running bioinf…Taverna: a tool for building and running workflows of services (2006)AiiDA: automated interactive infrastructure and database for computational science (2015)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)Workflow Patterns (2003)Capturing and querying workflow runtime provenance with PROV (2013)Dynamic steering of HPC scientific workflows: A survey (2014)Human Information Processing (2016)Scientific Workflows (2016)Bioconductor: open software development for computational biology and bioinformatics (2004)Architecting a Distributed Bioinformatics Platform with iRODS and iPlant Agave API (2015)Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments (2017)Design Patterns: Elements of Reusable Object-Oriented Software (1994)Snakemake—a scalable bioinformatics workflow engine (2012)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)snakePipes: facilitating flexible, scalable and integrative epigenomic analysis (2019)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Reproducibility: A tragedy of errors (2016)Sustainable data analysis with Snakemake (2021)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The nf-core framework for community-curated bioinformatics pipelines (2020)Nextflow in Bioinformatics: Executors Performance Comparison Using Genomics Data (2023)What does research reproducibility mean? (2016)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Practical Computational Reproducibility in the Life Sciences (2017)Scientific workflows: Past, present and future (2017)BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows (2019)
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References

  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 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
  • 2013Ten Simple Rules for Reproducible Computational Research875 cited
  • 2013The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud678 cited
  • 2016A review of bioinformatic pipeline frameworks250 cited
  • 2016Common Workflow Language, draft 3204 cited
  • 2012Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support120 cited
  • 2014Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses81 cited

Cited by

  • 2021Using prototyping to choose a bioinformatics workflow management system28 cited
  • 2022H3AGWAS: a portable workflow for genome wide association studies17 cited
  • 2019Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience12 cited
  • 2020Publishing reproducible dynamic kinetic models12 cited
  • 2021The H3Africa Consortium: Publication Outputs of a Pan-African Genomics Collaboration (2013 to 2020)

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9 cited