CandidalysinModel

Repository Structure

• fitting.py: This file includes a collection of functions related to model fitting. It encompasses an abstract class for fitting models, computing validation intervals, and objective functions.

• model.py: The core model definition for the ODE models used.

• model_utils.py: This utility file provides wrapper functions for model fitting. Key features include simulating synthetic data for testing and evaluating the likelihood function of models.

• preprocessing.py: Preprocessing of data for fitting. This file contains methods and utilities for data cleaning, transformation, and preparation, ensuring that the data is in the right format for fitting.

• publication_figures.ipynb: A Jupyter Notebook for generating all the tables and figures given in the publication.

• requirements.txt: This file lists all the dependencies required to set up a Conda environment for running the scripts and the Jupyter Notebook included in this repository.

• script_screening.py: This script is dedicated to conducting parameter fitting on the data. It includes functionalities for parameter screening and optimization to enhance model accuracy and performance.

Installation

1. Clone the repository: git clone [repository-url]

2. Set up a Conda environment: conda create --name [env-name] --file requirements.txt

3. Activate the environment: conda activate [env-name]

License

This project is licensed under BSD - see the LICENSE file for details.

Data availability

Data can be accessed under ASBDATA