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Ten simple rules for documenting scientific software
6 references·15 citing·40 second hop
Ten simple rules for documenting scientific software (2018)Ten simple rules for documenting scientif…Ten Simple Rules for Developing Usable Software in Computational Biology (2017)Ten Simple Rules for Developi…Ten Simple Rules for Taking Advantage of Git and GitHub (2016)Ten Simple Rules for Taking A…A Quick Introduction to Version Control with Git and GitHub (2016)A Quick Introduction to Versi…Best Practices for Scientific Computing (2014)Best Practices for Scientific…Ten Simple Rules for the Open Development of Scientific Software (2012)Ten Simple Rules for the Open…A Quick Guide to Organizing Computational Biology Projects (2009)A Quick Guide to Organizing C…Reviewability and supportability: New complementary principles to empower research software practices (2024)Reviewability and supportabil…Good modelling software practices (2024)Good modelling software pract…ENCORE: a practical implementation to improve reproducibility and transparency of computational research (2024)ENCORE: a practical implement…Ten simple rules for researchers who want to develop web apps (2022)Ten simple rules for research…Ten simple rules for making a software tool workflow-ready (2022)Ten simple rules for making a…Documenting research software in engineering science (2022)Documenting research software…Advancing code sharing in the computational biology community (2022)Advancing code sharing in the…A call for clean code to effectively communicate science (2022)A call for clean code to effe…Ten simple rules on writing clean and reliable open-source scientific software (2021)Ten simple rules on writing c…Dealing with software complexity in individual‐based models (2021)Dealing with software complex…An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action (2021)An environment for sustainabl…Ten simple rules for writing a paper about scientific software (2020)Ten simple rules for writing …Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites (2020)Can reproducibility be improv…An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action (2020)An environment for sustainabl…Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software (2019)Bionitio: demonstrating and f…Computational science: ...Error (2010)Better Software, Better Research (2014)Four simple recommendations to encourage best practices in research software (2017)Challenges and recommendations to improve the installability and archival stability of omics computational tools (2019)Making scientific computations reproducible (2000)Scientific Software Development Is Not an Oxymoron (2006)Robust Modeling in Cognitive Science (2019)A Beginner's Guide to Conducting Reproducible Research (2021)Eleven quick tips for data cleaning and feature engineering (2022)Git can facilitate greater reproducibility and increased transparency in science (2013)Tools and techniques for computational reproducibility (2016)Ten simple rules for making research software more robust (2017)Toward standard practices for sharing computer code and programs in neuroscience (2017)WaveLab and Reproducible Research (1995)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)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)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)Improving the usability and archival stability of bioinformatics software (2019)A Practical Guide to Metabolomics Software Development (2021)An index to quantify an individual's scientific research output (2005)Astrophysics Source Code Library (2012)The role of metadata in reproducible computational research (2021)What Do We (Not) Know About Research Software Engineering? (2022)Toward Good Simulation Practice (2024)1,500 scientists lift the lid on reproducibility (2016)PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation (2018)The nf-core framework for community-curated bioinformatics pipelines (2020)Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice (2023)Good enough practices in scientific computing. (2017)Toward practical transparent verifiable and long-term reproducible research using Guix (2022)Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology (2023)Toward open science in marketing research (2024)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)Bayesian Inversion with Open-Source Codes for Various One-Dimensional Model Problems in Computational Mechanics (2022)Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering (2023)Reproducible research policies and software/data management in scientific computing journals: a survey, discussion, and perspectives (2025)
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References

  • 2014Best Practices for Scientific Computing715 cited
  • 2016Ten Simple Rules for Taking Advantage of Git and GitHub231 cited
  • 2016A Quick Introduction to Version Control with Git and GitHub194 cited
  • 2012Ten Simple Rules for the Open Development of Scientific Software143 cited
  • 2009A Quick Guide to Organizing Computational Biology Projects95 cited
  • 2017Ten Simple Rules for Developing Usable Software in Computational Biology84 cited

Cited by

  • 2021An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action41 cited
  • 2021Ten simple rules on writing clean and reliable open-source scientific software41 cited
  • 2020An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action36 cited
  • 2020Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites34 cited
  • 2021Dealing with software complexity in individual‐based models33 cited
  • 2022A call for clean code to effectively communicate science25 cited
  • 2019Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software20 cited
  • 2022Ten simple rules for making a software tool workflow-ready

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18 cited
  • 2022Advancing code sharing in the computational biology community16 cited
  • 2022Ten simple rules for researchers who want to develop web apps15 cited
  • 2024ENCORE: a practical implementation to improve reproducibility and transparency of computational research11 cited
  • 2022Documenting research software in engineering science11 cited
  • 2024Good modelling software practices10 cited
  • 2020Ten simple rules for writing a paper about scientific software9 cited
  • 2024Reviewability and supportability: New complementary principles to empower research software practices5 cited