STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability.

Sandra Díaz-Seoane, Xabier Rey Barreiro, Alejandro F Villaverde
Author Information
  1. Sandra Díaz-Seoane: Department of Systems and Control Engineering, Universidade de Vigo, Galicia, 36310 Vigo, Spain. ORCID
  2. Xabier Rey Barreiro: Department of Systems and Control Engineering, Universidade de Vigo, Galicia, 36310 Vigo, Spain. ORCID
  3. Alejandro F Villaverde: Department of Systems and Control Engineering, Universidade de Vigo, Galicia, 36310 Vigo, Spain. ORCID

Abstract

MOTIVATION: STRIKE-GOLDD is a toolbox that analyses the structural identifiability and observability of possibly non-linear, non-rational ODE models that may have known and unknown inputs. Its broad applicability comes at the expense of a lower computational efficiency than other tools.
RESULTS: STRIKE-GOLDD 4.0 includes a new algorithm, ProbObsTest, specifically designed for the analysis of rational models. ProbObsTest is significantly faster than the previously available FISPO algorithm when applied to computationally expensive models. Providing both algorithms in the same toolbox allows combining generality and computational efficiency. STRIKE-GOLDD 4.0 is implemented as a Matlab toolbox with a user-friendly graphical interface.
AVAILABILITY AND IMPLEMENTATION: STRIKE-GOLDD 4.0 is a free and open-source tool available under a GPLv3 license. It can be downloaded from GitHub at https://github.com/afvillaverde/strike-goldd.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

References

  1. Bioinformatics. 2018 Apr 15;34(8):1421-1423 [PMID: 29206901]
  2. PLoS Comput Biol. 2016 Oct 28;12(10):e1005153 [PMID: 27792726]
  3. Bioinformatics. 2023 Feb 3;39(2): [PMID: 36721336]
  4. Comput Methods Programs Biomed. 2007 Oct;88(1):52-61 [PMID: 17707944]
  5. J R Soc Interface. 2019 Jul 26;16(156):20190043 [PMID: 31266417]
  6. Bioinformatics. 2019 Aug 15;35(16):2873-2874 [PMID: 30601937]
  7. PLoS One. 2014 Oct 28;9(10):e110261 [PMID: 25350289]

Grants

  1. RYC-2019-027537-I/PREDYCTBIO
  2. /Consellería de Cultura, Educación e Ordenación Universitaria
  3. /Universidade de Vigo/CISUG

MeSH Term

Software
Algorithms

Word Cloud

Created with Highcharts 10.0.0STRIKE-GOLDD4toolboxmodels0availablestructuralidentifiabilityobservabilitycomputationalefficiencyalgorithmProbObsTestanalysisuser-friendlyMOTIVATION:analysespossiblynon-linearnon-rationalODEmayknownunknowninputsbroadapplicabilitycomesexpenselowertoolsRESULTS:includesnewspecificallydesignedrationalsignificantlyfasterpreviouslyFISPOappliedcomputationallyexpensiveProvidingalgorithmsallowscombininggeneralityimplementedMatlabgraphicalinterfaceAVAILABILITYANDIMPLEMENTATION:freeopen-sourcetoolGPLv3licensecandownloadedGitHubhttps://githubcom/afvillaverde/strike-golddSUPPLEMENTARYINFORMATION:SupplementarydataBioinformaticsonline0:efficient

Similar Articles

Cited By