SoBioS: A MATLAB repository from americocunhajr

Sobol' Indices for Biological Systems

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.

Overview
Features
UQLab dependency
Usage
Documentation
Authors
Citing SoBioS
License
Institutional support
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.

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:

Clone the repository:

git clone https://github.com/americocunhajr/SoBioS.git

Navigate to the code directory:
```
cd SoBioS/SoBioS-1.0
```
To run a simulation, execute the main file corresponding to your case:
```
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

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

@incollection{Tosin2020SoBioS,
   author    = {M. Tosin and A. M. A. C\ˆ{o}rtes and A. {Cunha~Jr}},
   title     = {A {T}utorial on {S}obol’ {G}lobal {S}ensitivity {A}nalysis {A}pplied to {B}iological {M}odels},
   editor    = {F.A.B. {da Silva} and N. Carels and M. {Trindade dos Santos} and F.J.P. Lopes},
   booktitle = {Networks in Systems Biology: Applications for Disease Modeling},
   publisher = {Springer International Publishing},
   address   = {Cham},
   year      = {2020},
   pages     = {93-118},
   doi       = {https://doi.org/10.1007/978-3-030-51862-2_6},
}

License

SoBioS is released under the MIT license. See the LICENSE file for details. All new contributions must be made under the MIT license.

americocunhajr/SoBioS