Welcome

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Figure 5.2. Sharing as part of the workflowFigure credits: Tomasz Zielinski and Andrés Romanowski

Introduction to Open Science

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Figure 1. Open Science Building Blocks

Being FAIR

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  • Figure 1. Impossible Protocol

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  • Depending on the software used to open (and the way the pdf was created), the local machine international settings, copying the data into Excel can bring unexpected results Figure 2. Pdf data copied to Excel
    Data needs parsing after coping to Excel Figure 2. The same data copied to Excel with polish locale
    The same data copied to Excel with polish locale has been converted to dates

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    Figure 2. FAIR principles After SangyaPundir

    Intellectual Property, Licensing and Openness

    Introduction to metadata

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    nematode_confocal_microscopy_imageFigure credits: María Eugenia Goya

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    Here we have an excel spreadsheet that contains project metadata for a made-up experiment of plant metabolites Metadata in data table exampleFigure credits: Tomasz Zielinski and Andrés Romanowski

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  • Structural metadata marked in green metadata-full-spreadhseetFigure credits: Tomasz Zielinski and Andrés Romanowski

    • Being precise

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    Why we need ORCID

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    The second metadata example (the Excel table): contains two other types of public IDs.
    Metadata in data table exampleFigure credits: Tomasz Zielinski and Andrés Romanowski

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    UI with controlled vocabularyExample of graphical user interfaces with controlled vocabularies

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    ontology-example

    (Meta)data in Excel

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    bad-metadata

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    White et al.

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  • Column L bad-metadata

    • Laboratory records

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    handwritten-tea-protocol
    Figure credits: Ines Boehm and Ben Thomas

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    handwritten-tea-protocol
    Figure credits: Ines Boehm and Ben Thomas

    Working with files

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    Intro to folder structureFigure credits: Andrés Romanowski

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    Have a look at the four different folder structures. file-organisation-strategiesFigure credits: Ines Boehm

    Reusable analysis

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    Select the notebook titled ‘student_notebook_light_conditions.ipynb’ as depicted below and click ‘Duplicate’. Confirm with Duplicate when you are asked if you are certain that you want to duplicate the notebook. Figure 1. Duplicate a Jupyter notebookFigure 1. Duplicate a Jupyter notebook

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    A copy of the notebook has appeared with the suffix ‘-Copy’ and a number (Figure 2a), select this notebook. Have a look around the notebook and explore its anatomy (Figure 2), you should see experimental details, an image, and code. If you click on separate parts of the notebook you can see that it is divided into individual cells (Figure 2 e-g) which are of varying type (Code, R in this case, or Markdown - Figure 2d). Hashtags are comments within the code and shall help you to interpret what individual bits of code do. Figure 2. Anatomy of a Jupyter notebook: (a) depicts the name of thenotebook, (b, c) are toolbars, (c) contains the most commonly usedtools, (d) shows of what type - Markdown, Code etc... - the currentlyselected cell is, and (e-g) are examples of cells, where (e) shows thecurrently selected cell.Figure 2. Anatomy of a Jupyter notebook: (a) depicts the name of the notebook, (b, c) are toolbars, (c) contains the most commonly used tools, (d) shows of what type - Markdown, Code etc… - the currently selected cell is, and (e-g) are examples of cells, where (e) shows the currently selected cell.

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    If you followed all steps correctly you should have reproduced the table, a graph and statistical testing. Apart from the pre-filled markdown text the rendered values of the code should look like this: Figure 3. Rendering of data frameFigure 3. Rendering of data frame Figure 4. Rendering of plotFigure 4. Rendering of plot

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    Figure 5. Advanced PlotFigure 5. Short- and long-day light conditions depicted as a grouped boxplot

    Version control

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    Figure 1. Versioning Hell
    from: Wit and wisdom from Jorge Cham (http://phdcomics.com/)

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    Figure 2. How VCS works


    from: Version control with git (https://carpentries-incubator.github.io/git-novice-branch-pr/01-basics/)

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    Figure 3. Using Git
    from: xkcd (https://xkcd.com/1597/)

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    Figure 4. Semantic versioning
    from: Semantic versioning, Parikshit Hooda (https://www.geeksforgeeks.org/introduction-semantic-versioning/)

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    Figure 5. Semantic versioning
    from: Semantic versioning, Parikshit Hooda (https://www.geeksforgeeks.org/introduction-semantic-versioning/)

    Templates for consistency

    Public repositories

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    DOI

    It's all about planning

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    Figure 5.1. The Research Data Life CycleFigure credits: Tomasz Zieliński

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    Figure 5.3. Planning aheadFigure credits: Tomasz Zieliński and Andrés Romanowski

    Putting it all together

    Template

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    Figure 1. I am some figure