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Using the app

The app has four tabs. Only the selected tab is computed, and every tab has its own link: the tab is part of the address, e.g., faircombine.streamlit.app/?tab=Indicators, and on Example Assessments also the model, e.g., ?tab=Example+Assessments&model=PMR_curated.

About

The motivation of the FAIR COMBINE Archive Indicators, how to cite the publication and the app, and an example of the Model and Model metadata indicators of the BioModels_C19_curated assessment.

Assess Model

Assess your own model:

  1. Download the template with Download FAIR template.
  2. Fill in the column Assessment for every indicator, see Assessing a model.
  3. Upload the filled template with Upload FAIR model assessment, at most 1 MB.

The app shows the FAIR percentage per category as a bar plot, one polar bar plot per type of indicator (Model, Model metadata, Archive, Archive metadata), and the table of the assessment. In the polar bar plots an indicator which does not apply to the model (NA) is a full gray bar, an indicator assessed with 0 has no bar; see Scoring for the percentages. A file which is not a filled template, misses or adds indicators, or has an assessment value other than empty, 0, 0.5 or 1 is reported as an error naming the columns or the indicators. Only the column Assessment is taken from the file, the description of the indicators always comes from the template. The uploaded file stays selected when you switch tabs.

Below the upload, Export figure downloads the assessment as one figure, see Exporting a figure.

The uploaded file is only processed in the running app: it is never written to disk, never shared with other users of the app and is discarded when you close the page.

Example Assessments

The assessments bundled with the app, e.g., curated and non curated models of BioModels and the Physiome Model Repository and published pharmacokinetic models. Select a model to show the same plots as for an uploaded assessment and to export them with Export figure.

Exporting a figure

Export figure downloads the bar plot and the four polar bar plots of an assessment as one figure, e.g., for a manuscript or a presentation. Choose the format with Export format:

  • PNG and JPEG: 3000 x 4200 pixels, 300 dpi at a width of 10 inches.
  • SVG and PDF: vector graphics, which stay sharp at any size and can be edited, e.g., in Inkscape.

The title names the model, the name of the uploaded file or of the example assessment, which is also the file name, e.g., my_model_FAIR-CA.pdf. The figure states the version of the app and its DOI, e.g., fair-ca-visualization 0.5.0, https://doi.org/10.5281/zenodo.13755820, so a figure in a manuscript can be referred to as "FAIR assessment of model X, visualized with fair-ca-visualization 0.5.0". Please also cite the app and the FAIR COMBINE Archive Indicators as described on the About tab.

The figure is rendered on the server with kaleido, which needs Chrome or Chromium. The deployed app has it; a local installation uses an installed Chrome or Chromium, or one installed with plotly_get_chrome. Without one Export figure is disabled. A single plot can also be saved from the plot itself with the camera icon above it, as PNG at screen resolution.

Indicators

All indicators of the template with their identifier, short label, type, category, priority and the question the indicator asks. The columns NA, 0, 0.5 and 1 count the example assessments which rate the indicator with that value.