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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.

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/ directory.

Download & installation

Clone the PESTO repository or download the latest release archive. 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. Further documentation is available in 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 file in the PESTO source directory.