models

Models prepared for CLUE

This folder contains models that can be read directly with CLUE in order to perform exact reduction. Each model is specified in *.ode format (see ERODE).

The folder is split into two different classes of models:

• Polynomial models: the folder polynomial contains the example models with Polynomial dynamics. This means that the corresponding differential system has a polynomial right-hand side and a direct approach can be used (see this paper).
• Rational models: the folder rational contains the example models with Rational dynamics, i.e., the differential systems associated with them have a right-hand side with rational functions. CLUE provides both a deterministic and a probabilistic approach to handle these models (see this paper).

Check the README files in each folder for a further detail and documentation on each of the models.

We include the file data.json file to unify the access to these models and provide an easy way to update the database in the future. Also, the script models_data.py will update the README.md files in the inner folders to include the new models and references. With all of these, in order to add a new model the following procedure must be done:

1. Add the .ode file to the corresponding folder.
2. Add the data to data.json with the following fields:
   • Name: must coincide with the name of the folder
   • Type: either polynomial or rational. This indicates the folder to find the model.
   • Range: in case there are several files associated with this model. The name of the .ode files must be "{name}({range})".
   • Reference (title): title of the reference paper. May be empty.
   • Reference (doi): doi link to the reference paper. May be empty.
3. Run in this folder the script models_data.py by using the command python3 models_data.py.