Data analysis

Now so far I’ve just added the raw data. How can I describe how I analyzed my data and created results?

The ARC offers different options to annotate and perform data analysis.

A computational workflow is like a protocol

Section titled A computational workflow is like a protocol

Just like laboratory workflows produce samples or data, computational workflows produce data. They represent the processing steps used in data analysis or data transformation.

Option I: Create a virtual assay

Section titled Option I: Create a virtual assay

A computational workflow can simply be treated as a protocol. This can be a summary of the steps followed in any data analysis software. Or it can be a script. Hence the data analysis can simply be packaged as an assay, with the computational workflow stored in protocols and the resulting data stored in dataset

ARCitect

1. Add a new assay Visualization.

2. Import the python script heatmap.py into protocols.

3. Import the figure heatmap.svg resulting from the script into dataset.

   • Directoryassays

     • DirectoryVisualization

       • Directorydataset

         • heatmap.svg
       • Directoryprotocols

         • heatmap.py
       • isa.assay.xlsx
       • README.md
   • …

4. Add a new annotation table to Visualization.

5. Add the following building blocks:

   • Input [Data]: Use File Picker to reference the proteomics output file.
   • Protocol REF: Use File Picker to reference python script.
   • Output [Data]: Use File Picker to reference to heatmap result file.

   Input [Data]	ProtocolREF	Output [Data]
   sugar_result.csv	heatmap.py	heatmap.svg

Option II: Create a run and a workflow

Section titled Option II: Create a run and a workflow

If your data analysis is code-based, you likely aim to make it reusable and actionable in-place. To achieve this, we recommend to wrap and annotate your workflow using Common Workflow Language (CWL). Although CWL is out of the scope of this starters’ guide, we want to share the basic concept here.

• In the ARC the computational workflow is placed in the workflows folder.
• The results produced from workflows are stored in runs. Every time a workflow is employed, it creates a new run result.

CWL abstract – documents to describe your computational workflows

Section titled CWL abstract – documents to describe your computational workflows

The scipt file in workflows is accompanied with a CWL file, which contains workflow metadata to render it reusable. The specific parameters of a run’s execution are stored in a separate job file.