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https://github.com/americocunhajr/sobios
SoBioS is an easy-to-run Matlab code to compute Sobol' indices for biological systems.
https://github.com/americocunhajr/sobios
bioinformatics biomathematics computational-biology dynamical-systems global-sensitivity-analysis nonlinear-dynamics sensitivity-analysis sobol-indices uerj ufrj
Last synced: 12 days ago
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SoBioS is an easy-to-run Matlab code to compute Sobol' indices for biological systems.
- Host: GitHub
- URL: https://github.com/americocunhajr/sobios
- Owner: americocunhajr
- License: mit
- Created: 2020-03-31T04:49:26.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-07-18T03:41:58.000Z (4 months ago)
- Last Synced: 2024-07-19T02:24:08.144Z (4 months ago)
- Topics: bioinformatics, biomathematics, computational-biology, dynamical-systems, global-sensitivity-analysis, nonlinear-dynamics, sensitivity-analysis, sobol-indices, uerj, ufrj
- Language: MATLAB
- Homepage: https://americocunhajr.github.io/SoBioS
- Size: 14.6 MB
- Stars: 6
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
## 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](#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.
### 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/americocunhajr/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
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
