Introduction to Open Science and FAIR principles

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Figure 1. Open Science Building Blocks
Figure 1. Open Science Building Blocks

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Figure 1. Impossible Protocol
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

    • Figure 4

    Figure 2. FAIR principles After SangyaPundir

    Introduction to metadata

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    nematode_confocal_microscopy_imageFigure credits: María Eugenia Goya

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    Metadata in data table example
    Figure credits: Tomasz Zielinski and Andrés Romanowski

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    Minimum information standards
    Figure. Some of the MIBBI minimum information standards from fairsharing.org

    Tidy (meta)data tables

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    bad-metadata
    bad-metadata

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    White et al.
    White et al.

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  • Column L bad-metadata

    • 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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    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.
    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 frame
    Figure 3. Rendering of data frame Figure 4. Rendering of plot
    Figure 4. Rendering of plot

    Public repositories

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    DOI

    Journey to be FAIR

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