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Building an Open Representation for Biological Protocols
9 references·5 citing·40 second hop
Building an Open Representation for Biological Protocols (2023)Building an Open Representation for Biolo…Aquarium: open-source laboratory software for design, execution and data management (2021)Aquarium: open-source laborat…Quantification of bacterial fluorescence using independent calibrants (2018)Quantification of bacterial f…Achieving Reproducibility and Closed-Loop Automation in Biological Experimentation with an IoT-Enabled Lab of the Future (2018)Achieving Reproducibility and…Toil enables reproducible, open source, big biomedical data analyses (2017)Toil enables reproducible, op…Protocols.io: Virtual Communities for Protocol Development and Discussion (2016)Protocols.io: Virtual Communi…Common Workflow Language, draft 3 (2016)Common Workflow Language, dra…Harnessing QbD, Programming Languages, and Automation for Reproducible Biology (2015)Harnessing QbD, Programming L…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…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…From FAIR to CURE: guidelines for computational models of biological systems (2026)From FAIR to CURE: guidelines…Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications (2025)Abstraction hierarchy to defi…Engineering biology and automation–Replicability as a design principle (2024)Engineering biology and autom…An engineering biology approach to automated workflow and biodesign (2024)An engineering biology approa…The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology (2023)The Laboratory Automation Pro…Taverna: a tool for building and running workflows of services (2006)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)Design Patterns: Elements of Reusable Object-Oriented Software (1994)Bioconductor: open software development for computational biology and bioinformatics (2004)Snakemake—a scalable bioinformatics workflow engine (2012)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Nextflow enables reproducible computational workflows (2017)Design of Experiments (1936)On the Experimental Attainment of Optimum Conditions (1951)Power failure: why small sample size undermines the reliability of neuroscience (2013)Intensified design of experiments for upstream bioreactors (2016)Automated Planning Enables Complex Protocols on Liquid-Handling Robots (2018)OpenWorkstation: A modular open-source technology for automated in vitro workflows (2020)Galaxy: A platform for interactive large-scale genome analysis (2005)The iPlant Collaborative: Cyberinfrastructure for Plant Biology (2011)A multi-disciplinary perspective on emergent and future innovations in peer review (2017)Integrating “Big Data” into Aquatic Ecology: Challenges and Opportunities (2017)What is missing in autonomous discovery: open challenges for the community (2023)Biotech giant publishes failures to confirm high-profile science (2016)A manifesto for reproducible science (2017)Improving Reproducibility in Synthetic Biology (2019)Integrating autonomy into automated research platforms (2023)A property graph schema for automated metadata capture, reproducibility and knowledge discovery in high-throughput bioprocess development (2025)Why Most Published Research Findings Are False (2005)Why Most Published Research Findings Are False (2005)1,500 scientists lift the lid on reproducibility (2016)Support academic access to automated cloud labs to improve reproducibility (2023)Towards a modular architecture for science factories (2023)openBIS ELN-LIMS: an open-source database for academic laboratories (2015)SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology (2018)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Sustainable data analysis with Snakemake (2021)Methods included (2022)Advancing reproducibility can ease the ‘hard truths’ of synthetic biology (2023)Data hazards in synthetic biology (2024)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

  • 2010Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences3,455 cited
  • 2017Toil enables reproducible, open source, big biomedical data analyses1,362 cited
  • 2013The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud678 cited
  • 2016Common Workflow Language, draft 3204 cited
  • 2016Protocols.io: Virtual Communities for Protocol Development and Discussion90 cited
  • 2018Quantification of bacterial fluorescence using independent calibrants74 cited
  • 2015Harnessing QbD, Programming Languages, and Automation for Reproducible Biology52 cited
  • 2018Achieving Reproducibility and Closed-Loop Automation in Biological Experimentation with an IoT-Enabled Lab of the Future45 cited
  • 2021Aquarium: open-source laboratory software for design, execution and data management40 cited

Cited by

  • 2025Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications21 cited
  • 2023The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology13 cited
  • 2026From FAIR to CURE: guidelines for computational models of biological systems8 cited
  • 2024An engineering biology approach to automated workflow and biodesign7 cited

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  • 2024Engineering biology and automation–Replicability as a design principle6 cited