Suppr超能文献

PESTO：参数估计工具箱。

PESTO: Parameter EStimation TOolbox.

机构信息

Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.

Center for Mathematics, Technische Universität München, 85748 Garching, Germany.

出版信息

Bioinformatics. 2018 Feb 15;34(4):705-707. doi: 10.1093/bioinformatics/btx676.

DOI:10.1093/bioinformatics/btx676
PMID:29069312
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5860618/
Abstract

SUMMARY

PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability 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, for which the user can provide a deterministic objective function in MATLAB.

AVAILABILITY AND IMPLEMENTATION

PESTO is a MATLAB toolbox, freely available under the BSD license. The source code, along with extensive documentation and example code, can be downloaded from https://github.com/ICB-DCM/PESTO/.

CONTACT

jan.hasenauer@helmholtz-muenchen.de.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

摘要

PESTO 是一个广泛适用且高度可定制的 MathWorks MATLAB 参数估计工具包。它提供了可扩展的算法，用于优化、不确定性和可识别性分析，这些算法以非常通用的方式工作，将目标函数视为黑盒。因此，PESTO 可用于任何参数估计问题，用户可以在 MATLAB 中提供确定性目标函数。

可用性和实现

PESTO 是一个 MATLAB 工具箱，根据 BSD 许可证免费提供。源代码以及详细的文档和示例代码可从 https://github.com/ICB-DCM/PESTO/ 下载。

联系人

jan.hasenauer@helmholtz-muenchen.de。

补充信息

补充数据可在“Bioinformatics”在线获取。

相似文献

1
PESTO: Parameter EStimation TOolbox.
Bioinformatics. 2018 Feb 15;34(4):705-707. doi: 10.1093/bioinformatics/btx676.
2
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.
Bioinformatics. 2018 Apr 15;34(8):1421-1423. doi: 10.1093/bioinformatics/btx735.
3
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.
Bioinformatics. 2018 Jul 1;34(13):i151-i159. doi: 10.1093/bioinformatics/bty230.
4
Parameter estimation for dynamical systems with discrete events and logical operations.
Bioinformatics. 2017 Apr 1;33(7):1049-1056. doi: 10.1093/bioinformatics/btw764.
5
Hierarchical optimization for the efficient parametrization of ODE models.
Bioinformatics. 2018 Dec 15;34(24):4266-4273. doi: 10.1093/bioinformatics/bty514.
6
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models.
Bioinformatics. 2023 Nov 1;39(11). doi: 10.1093/bioinformatics/btad711.
7
An easy and efficient approach for testing identifiability.
Bioinformatics. 2018 Jun 1;34(11):1913-1921. doi: 10.1093/bioinformatics/bty035.
8
A scalable moment-closure approximation for large-scale biochemical reaction networks.
Bioinformatics. 2017 Jul 15;33(14):i293-i300. doi: 10.1093/bioinformatics/btx249.
9
STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability.
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac748.
10
A Cytoscape app for motif enumeration with ISMAGS.
Bioinformatics. 2017 Feb 1;33(3):461-463. doi: 10.1093/bioinformatics/btw626.

引用本文的文献

1
Reducing phenotype-structured partial differential equations models of cancer evolution to systems of ordinary differential equations: a generalised moment dynamics approach.
J Math Biol. 2025 Jul 28;91(2):22. doi: 10.1007/s00285-025-02246-5.
2
The Constrained Disorder Principle Overcomes the Challenges of Methods for Assessing Uncertainty in Biological Systems.
J Pers Med. 2024 Dec 28;15(1):10. doi: 10.3390/jpm15010010.
3
Mathematical multi-compartment modeling of chronic lymphocytic leukemia cell kinetics under ibrutinib.
iScience. 2024 Oct 28;27(12):111242. doi: 10.1016/j.isci.2024.111242. eCollection 2024 Dec 20.
4
A Model-Driven Meta-Analysis Supports the Emerging Consensus View that Inhibitory Neurons Dominate BOLD-fMRI Responses.
bioRxiv. 2024 Oct 17:2024.10.15.618416. doi: 10.1101/2024.10.15.618416.
5
analysis of design of experiment methods for metabolic pathway optimization.
Comput Struct Biotechnol J. 2024 May 3;23:1959-1967. doi: 10.1016/j.csbj.2024.04.062. eCollection 2024 Dec.
6
DataXflow: Synergizing data-driven modeling with best parameter fit and optimal control - An efficient data analysis for cancer research.
Comput Struct Biotechnol J. 2024 Apr 8;23:1755-1772. doi: 10.1016/j.csbj.2024.04.010. eCollection 2024 Dec.
7
Bayesian Regression Facilitates Quantitative Modeling of Cell Metabolism.
ACS Synth Biol. 2024 Apr 19;13(4):1205-1214. doi: 10.1021/acssynbio.3c00662. Epub 2024 Apr 5.
8
Modeling early treatment response in AML from cell-free tumor DNA.
iScience. 2023 Oct 19;26(12):108271. doi: 10.1016/j.isci.2023.108271. eCollection 2023 Dec 15.
9
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models.
Bioinformatics. 2023 Nov 1;39(11). doi: 10.1093/bioinformatics/btad711.
10
Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load.
PLoS Comput Biol. 2023 Aug 24;19(8):e1011425. doi: 10.1371/journal.pcbi.1011425. eCollection 2023 Aug.

本文引用的文献

1
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.
PLoS Comput Biol. 2017 Jan 23;13(1):e1005331. doi: 10.1371/journal.pcbi.1005331. eCollection 2017 Jan.
2
Analysis of CFSE time-series data using division-, age- and label-structured population models.
Bioinformatics. 2016 Aug 1;32(15):2321-9. doi: 10.1093/bioinformatics/btw131. Epub 2016 Mar 8.
3
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
BMC Bioinformatics. 2014 May 10;15:136. doi: 10.1186/1471-2105-15-136.
4
Lessons learned from quantitative dynamical modeling in systems biology.
PLoS One. 2013 Sep 30;8(9):e74335. doi: 10.1371/journal.pone.0074335. eCollection 2013.
5
High-dimensional Bayesian parameter estimation: case study for a model of JAK2/STAT5 signaling.
Math Biosci. 2013 Dec;246(2):293-304. doi: 10.1016/j.mbs.2013.04.002. Epub 2013 Apr 16.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验