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Infrastructures for Reproducible and Transparent Scholarly Communication Markus Konkol 1 , Daniel Nüst 1 , Laura Goulier 1 1 Institute for Geoinformatics (ifgi), D-48149 Münster, Germany E p What do I need? - Platform hosting - Choice of License - Stage of the project - Funding - Supported research areas - Supported submission formats - Upload - Copyright Support of: - Searching - Inspection - Download - Execution - Manipulation - Storing - Modification/ Deletion after publication - Sharing Konkol et al. (2020): Publishing computational Research - A review of infrastructures for reproducible and transparent scholarly communication. arXiv: 2001.00484 Reader Author Library Publisher ReproZip Provides a set of CLI commands for encapsulating the analysis. It can be executed on a provided server or locally Whole Tale Create a “Tale” for the analysis requirements so users can inspect and execute it in the original environment in browser o2r Provides one-click reproduction to manipulate parameters and compare results. Binder Launch analyses from Binder-ready repository and inspect the workflow in the browser Code Ocean Commercial platform to create “capsules” for several programming languages. Inspect, execute and manipulate the analysis in the browser eLife RDS Platform to publish scientific articles as executable documents with all code snippets on “Stencila” Galaxy Develop computational analyses without programming expertise using Jupyter Notebook Gigantum Packages analyses in Git repositories. Offers a commercial client application to create and execute analyses locally and a cloud to collaborate with peers Limitations ➔ Handling of sensitive (e.g. private) data solution: cloud based data enclaves or involvement of trustworthy authority ➔ Very large data sets and long computational times ➔ No guaranteed anonymity of authors within review process solution: anonymous version of the materials ➔ Need for specialised hardware ➔ Often no support for handling copyright ➔ Possibility of deleting materials after publication prevents permanent storage of code and data Manuscripts Online tool to write executable collaborative documents based on literate programming within a UI REANA Self-hosting platform that provides a set of CLI commands to run large analyses on a remote cloud Take-home messages 1. Many platforms provide one-click reproduction, e.g. o2r. 2. All platforms cover a broad range of stakeholder needs 3. You can use o2r to modify parameters and compare interactive Figures. INSPECT MANIPULATE Publishing open reproducible research is sustainable and fair. The trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results of scientific papers. Platforms provide solutions to support the publication of code and data. Trends ➔ Self-hosting of the infrastructure ➔ Support for notebooks (e.g. RMarkdown, Jupyter) ➔ Provision of UI or integrated development environment instead of CLI commands

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  • Infrastructures for Reproducible and Transparent Scholarly Communication

    Markus Konkol1, Daniel Nüst1, Laura Goulier11 Institute for Geoinformatics (ifgi), D-48149 Münster, Germany

    Ep

    What do I

    need?- Platform hosting- Choice of License- Stage of the project- Funding

    - Supported research areas- Supported submission

    formats- Upload- Copyright

    Support of: - Searching- Inspection- Download- Execution- Manipulation

    - Storing- Modification/

    Deletion after publication

    - Sharing

    Konkol et al. (2020): Publishing computational Research - A review of infrastructures for reproducible and transparent scholarly communication. arXiv: 2001.00484

    ReaderAuth

    or

    Librar

    yPublisher

    ReproZipProvides a set of CLI commands for encapsulating the analysis. It can be executed on a provided server or locally

    Whole TaleCreate a “Tale” for the analysis requirements so users can inspect and execute it in the original environment in browser

    o2rProvides one-click reproduction to manipulate parameters and compare results.

    BinderLaunch analyses from Binder-ready repository and inspect the workflow in the browser

    Code OceanCommercial platform to create “capsules” for several programming languages. Inspect, execute and manipulate the analysis in the browser

    eLife RDSPlatform to publish scientific articles as executable documents with all code snippets on “Stencila”

    GalaxyDevelop computational analyses without programming expertise using Jupyter Notebook

    GigantumPackages analyses in Git repositories. Offers a commercial client application to create and execute analyses locally and a cloud to collaborate with peers

    Limitations

    ➔ Handling of sensitive (e.g. private) data solution: cloud based data enclaves or involvement of trustworthy authority

    ➔ Very large data sets and long computational times➔ No guaranteed anonymity of authors within review process

    solution: anonymous version of the materials ➔ Need for specialised hardware➔ Often no support for handling copyright➔ Possibility of deleting materials after publication

    prevents permanent storage of code and data

    ManuscriptsOnline tool to write executable

    collaborative documents based on literate programming within a UI

    REANASelf-hosting platform that provides a set of CLI

    commands to run large analyses on a remote cloud

    Take-home messages

    1. Many platforms provide one-click reproduction, e.g. o2r.

    2. All platforms cover a broad range of stakeholder needs

    3. You can use o2r to modify parameters and compare

    interactive Figures.

    INSPECT

    MANIPULATE

    Publishing open reproducible research is sustainable and fair.

    The trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational

    results of scientific papers.

    Platforms provide solutions to support the publication of code and data.

    Trends

    ➔ Self-hosting of the infrastructure➔ Support for notebooks (e.g. RMarkdown, Jupyter)➔ Provision of UI or integrated development environment

    instead of CLI commands


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