Tutorials
Test files
Input files used to create publication data can be found here
Tutorial 1: Default Use (general extension)
This tutorial assumes that the input files are a model in the standard BioRECIPES format and an LEE set from REACH.
Tutorial 2: Specifying Score and Attributes
Tutorial 3: Using VIOLIN at the terminal
This tutorial assumes that the input files are a model in the standard BioRECIPES format and an LEE set from REACH. This tutorial also assumes that the user wants to run VIOLIN for basic extension using VIOLIN’s default values, and visualization is for the total output
The use_violin_script.py script is included in the examples folder. The input for this script allows for four classification schemes:
‘extend’ - default Kind and Match Score values for general extension
‘extend subcategories’ - general extension values with subcategories specified in Kind Score values
‘corroborate’ - Kind and Match Score values for general corroboration (preference towards strong corroborations, weak corroborations, contradictions)
‘corroborate subcategories’ - general extension values with subcategories specified in Kind Score values
as well as the same filtering options from Visualization (violin.visualize_violin)
To run use_violin_script.py at the command line:
python examples/use_violin_script.py examples/input/ModelA.csv examples/input/RA2_reading.xlsx examples/output extend 50%