Warming Stripes

Example to demonstrate executable nano publications:

• Nanopublication related to warming stripes 1950 - 2019, Freiburg (Germany): https://w3id.org/np/RAnqaMx3Ri3bR8yY3oiM-BeMJf8LPxidTSqyEpcHyXoLc

Freiburg's temperature anomaly data (1950-2019) was plotted with a replicable workflow as warming stripes, revealing a marked shift from blue (colder) to red (warmer) that demonstrates accelerating local warming.

• This nanopublication is an AIDA sentence that is supported by a figure (see below) and associated dataset and workflow:

Step 1: Get the workflow from an executable nanopublication

python galaxy_rocrate_finder.py https://w3id.org/np/RAnqaMx3Ri3bR8yY3oiM-BeMJf8LPxidTSqyEpcHyXoLc downloaded_rocrate

If the rocrate is found it is downloaded in downloaded_rocrate.

The workflow we will execute is shown below:

Step 2: Prepare inputs and parameters

This step will generate workflow.ga (exact copy of the workflow in the RO-Crate) and prepare the input parameters workflow_input_params.yml using data from the RO-Crate:

python prepare_inputs_and_parameters.py  9d075312-2f7b-4d24-850c-6cd3b3f1cd8a.zip  downloaded_workflows

Step 3: Run workflow with prepared inputs and parameters

Below we use planemo to send the data from the RO-Crate (copied locally) to Galaxy and execute the worfklow on the chosen galaxy instance:

planemo run workflow.ga workflow_input_params.yml --engine external_galaxy --galaxy_url https://usegalaxy.eu  --galaxy_user_key $GALAXY_API_KEY --history_name ScienceLive

This step assumes the tools used in the workflow are available in the selected Galaxy instance.

Step 4: Generate Markdown for new RO-Crate (optional)

python extract_md_from_galaxy_rocrate.py climate.rocrate.zip climate.rocrate.md

Step 5: Change inputs and rerun the workflow

Now we have shown the reproducibility of a workflow from a nanopublication containing an executable RO-Crate.

workflow.ga should not be changed. However, you can change workflow_input_params.yml for instance change the parameters for the stripes (name of the column to use for plotting, color, etc.) and/or change the input file too.

Change input datasets and parameters

• We will use the same workflow but for a different dataset and with a different colormap. For instance, to show the variation in the Annual percentage Change in popultation in Germany from 1950 to 2025.

• Source of data: Germany Population 1950-2025 (Macrotrends)

• Update the file workflow_input_params.yml:

files.tabular:
  class: File
  path: population/Germany-Population-Annual--Change-2025-05-27-15-17.csv
  filetype: csv
Column name to use for plotting: "Population"
Plot Title: Annual percentage Change for population in Germany (1950 - 2025)
nxsplit: null
xname (column name for the x-axis): null
Date/time format for the x-axis column: null
dates format for xlabels: null
Matplotlib colormap: Blues

Then we can run the workflow:

planemo run workflow.ga workflow_germany_params.yml --engine external_galaxy --galaxy_url https://usegalaxy.eu  --galaxy_user_key $GALAXY_API_KEY --history_name ScienceLive-Population-Germany

The resulting figure is shown below:

Step 6: Create RO-Crate (optional)

We can create a RO-Crate:

python create_rocreate.py --galaxy_url https://usegalaxy.eu  --galaxy_user_key $GALAXY_API_KEY --invocation-id 1d493693e187e30f --rocrate germany.rocrate.zip

Step 7: Generate Markdown for new RO-Crate (optional)

python extract_md_from_galaxy_rocrate.py germany.rocrate.zip germany.rocrate.md

Step 8: Archive in ROHub (or Zenodo):

python archive2rohub.py germany.rocrate.zip --md germany.rocrate.md 

The new workflow execution can then be archived for instance in Zenodo, ROHub or Workflowhub.eu: https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1382.1

Step 9: Create new nanopublication related to the new results (optional)

From the Figure and datasets we analysed, we can create a new AIDA sentence with supporting material (RO-Crate). For example, the corresponding AIDA sentence could be:

Germany’s population growth has varied over time, reflecting key historical events. Periods of increase, such as the post-war baby boom and labor migration in the 1960s, contrast with years of stagnation or decline, especially after reunification. More recent rises are linked to immigration and refugee inflows. The trend reveals how population change closely mirrors social and political shifts across decades.

This AIDA sentence can then be published in Nanodash AIDA Claims

The resulting nanopublication with the AIDA sentence and workflow execution is available at: https://w3id.org/np/RAJzZ8p6LBoe9D8ViX9DP2IIqZdxxfh-cQkBW3nfsYCzM