https://github.com/icb-dcm/pesto
PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
https://github.com/icb-dcm/pesto
matlab optimization parameter-estimation profile-likelihood systems-biology uncertainty-quantification
Last synced: 9 days ago
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PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
- Host: GitHub
- URL: https://github.com/icb-dcm/pesto
- Owner: ICB-DCM
- License: bsd-3-clause
- Created: 2016-04-05T09:58:04.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2020-03-02T12:42:04.000Z (about 5 years ago)
- Last Synced: 2025-04-11T09:52:17.187Z (about 1 month ago)
- Topics: matlab, optimization, parameter-estimation, profile-likelihood, systems-biology, uncertainty-quantification
- Language: MATLAB
- Homepage: https://doi.org/10.1093/bioinformatics/btx676
- Size: 248 MB
- Stars: 26
- Watchers: 8
- Forks: 12
- Open Issues: 42
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PESTO - Parameter EStimation TOolbox
PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers state-of-the art algorithms for optimization and uncertainty analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, which provides an objective function in MATLAB. PESTO has been used in various computational biology [research projects](https://github.com/ICB-DCM/PESTO/wiki#references).
PESTO features include:
* Multistart optimization
* Sampling routines
* Profile-likelihood analysis
* Visualization routines
* and more
These functions are demonstrated in several systems biology examples included in the [`examples/`](examples/) directory.
## Download & installation
Clone the PESTO repository or download the latest [release archive](https://github.com/ICB-DCM/PESTO/releases).
The top-level folder of the cloned repository or the unpacked archive needs to be added to the MATLAB search path (non-recursively).
*Note:* Detailed instructions on how to modify your MATLAB search path are provided here: https://de.mathworks.com/help/matlab/matlab_env/add-remove-or-reorder-folders-on-the-search-path.html
## Documentation
PESTO usage is demonstrated in various [examples](examples/). Further documentation is available in [```doc/PESTO-doc.pdf```](doc/PESTO-doc.pdf).
## Compatibility
PESTO is implemented fully in MATLAB and compatible with MATLAB releases from R2014b up to at least 2017a running on Windows, Mac and Linux.
## Citation
If you use PESTO in a projects, please cite
* Stapor, P., Weindl, D., Ballnus, B., Hug, S., Loos, C., Fiedler, A., Krause, S., Hross, S., Fröhlich, F., Hasenauer, J. (2018). PESTO: Parameter EStimation TOolbox. Bioinformatics, 34(4), 705-707. doi: 10.1093/bioinformatics/btx676
## Licensing
See [ ```LICENSE```](LICENSE) file in the PESTO source directory.