americocunhajr / SoBioS

SoBioS is an easy-to-run Matlab code to compute Sobol' indices for biological systems.

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.

Table of Contents

• 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:

1. Clone the repository:

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

2. Navigate to the code directory:

   cd SoBioS/SoBioS-1.0

3. 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.

Institutional support

   

Funding