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<img src="logo/SoBioS.png" width="40%">

**SoBioS: Sobol' Indices for Biological Systems** is an easy-to-run Matlab code used for Sobol' indices-based global sensitivity analysis of Biological Systems. The implementation follows an educational style, to make its use very intuitive.

This package includes the following modules:

- SoBioS_CaseName.m - main file for the simulation (use servaral resourses from UQLab package);
- QoI_CaseName.m - function to compute the Quantity of Interest (QoI).


## Software History

This code was developed as a pedagogical tool to teach the basics of global sensitivity analysis of biological systems via Sobol' indices. A tutorial explaining the theory and practical aspects behind **SoBioS** package is provided in the following book chapter:
- *Tosin M., Côrtes A.M.A., Cunha A. (2020) A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models. In: da Silva F.A.B., Carels N., Trindade dos Santos M., Lopes F.J.P. (eds) Networks in Systems Biology: Applications for Disease Modeling. Computational Biology, vol 32. Springer, Cham https://doi.org/10.1007/978-3-030-51862-2_6*
**SoBioS: Sobol' Indices for Biological Systems** is an easy-to-use Matlab code designed for Sobol' indices-based global sensitivity analysis of biological systems. Developed with an educational approach, **SoBioS** is intuitive and user-friendly, making it an excellent tool for researchers and students in the field of systems biology.

## Table of Contents
- [Overview](#overview)
- [Features](#features)
- [UQLab Dependency](#uqlab-dependency)
- [Usage](#usage)
- [Documentation](#documentation)
- [Authors](#authors)
- [Citing SoBioS](#citing-sobios)
- [License](#license)
- [Institutional Support](#institutional-support)
- [Funding](#funding)

## Overview
**SoBioS** was developed as a pedagogical tool to teach the basics of global sensitivity analysis of biological systems via Sobol' indices. A tutorial explaining the theory and practical aspects behind the **SoBioS** package is provided in the following book chapter:
- **M. Tosin, A.M.A. Côrtes, A. Cunha Jr**, *A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models*, in Networks in Systems Biology: Applications for Disease Modeling, Computational Biology, vol. 32, Springer, Cham, 2020. [DOI](https://doi.org/10.1007/978-3-030-51862-2_6)

## Features
- Global sensitivity analysis using Sobol' indices
- Easy-to-run Matlab implementation
- Educational style code for easy understanding
- Includes example cases and detailed comments

## UQLab dependency

In order to use the **SoBioS** code, it is necessary to have UQLab package installed:
https://www.uqlab.com

This external package is free for academic use.

## Usage
This package includes the following modules:
- SoBioS_CaseName.m - main file for the simulation (use servaral resourses from UQLab package);
- QoI_CaseName.m - function to compute the Quantity of Interest (QoI).

To get started with **SoBioS**, follow these steps:
1. Clone the repository:
```bash
git clone https://github.com/yourusername/SoBioS.git
```
2. Navigate to the code directory:
```bash
cd SoBioS/SoBioS-1.0
```
3. To run a simulation, execute the main file corresponding to your case:
```bash
SoBioS_CaseName
```
## Documentation
The routines in SoBioS are well-commented to explain their functionality. Each routine includes a description of its purpose, as well as inputs and outputs. Detailed documentation can be found within the code comments and the provided tutorial.

## Authors
- Michel Tosin
- Adriano Côrtes
- Americo Cunha

## Citing SoBioS

We kindly ask users to cite the following reference in any publications reporting work done with **SoBioS**:
If you use **SoBioS** in your research, please cite the following publication:
- *Tosin M., Côrtes A.M.A., Cunha A. (2020) A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models. In: da Silva F.A.B., Carels N., Trindade dos Santos M., Lopes F.J.P. (eds) Networks in Systems Biology: Applications for Disease Modeling. Computational Biology, vol 32. Springer, Cham https://doi.org/10.1007/978-3-030-51862-2_6*

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