STRIKE-GOLDD

STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition) is a MATLAB toolbox that analyses the local structural identifiability, observability, and invertibility of (possibly nonlinear) dynamic models of ordinary differential equations (ODEs).

Implementation and requirements

STRIKE-GOLDD is implemented in MATLAB. It requires:

* only required if one wishes to use optimization-based decomposition.

Download

The latest version of STRIKE-GOLDD can be downloaded from GitHub.

Older versions available upon request.

Contact

STRIKE-GOLDD is maintained by Alejandro F. Villaverde (CSIC). Email: afvillaverde@iim.csic.es; web: https://sites.google.com/site/alexfvillaverde/

Acknowledgements

STRIKE-GOLDD was initially developed by Alejandro F Villaverde during a stay at the University of Oxford with Antonis Papachristodoulou, and in collaboration with Antonio Barreiro (University of Vigo). The Lie symmetries code was written by Gemma Massonis Feixas (CSIC). The ORC-DF algorithm and the multi-experiment setup was written by Nerea Martínez (Univ. Vigo & CSIC). A number of collaborators have contributed to theoretical and/or application aspects: Neil D. Evans (Warwick Univ.), Michael J. Chappell (Warwick Univ.), Julio R. Banga (CSIC), and Nikolaos Tsiantis (CSIC).

Publications

STRIKE-GOLDD:

  • Villaverde AF, Barreiro A, Papachristodoulou A (2016). "Structural Identifiability of Dynamic Systems Biology Models". PLoS Computational Biology 12(10): e1005153. doi:10.1371/journal.pcbi.1005153

STRIKE-GOLDD2:

  • Villaverde AF, Evans ND, Chappell MJ, Banga JR (2019), "Input-dependent structural identifiability of nonlinear systems". IEEE Control Systems Letters 3(2):1–6. doi:10.1109/LCSYS.2018.2868608

STRIKE-GOLDDv2.1:

  • Villaverde AF, Tsiantis N, Banga JR (2019), "Full observability and estimation of unknown inputs, states, and parameters of nonlinear biological models ". Journal of the Royal Society Interface 16:20190043 . doi:10.1098/rsif.2019.0043

STRIKE-GOLDDv2.1.6:

  • G Massonis, AF Villaverde (2020) Finding and breaking Lie symmetries: implications for structural identifiability and observability in biological modelling. Symmetry, 12(3), 469 doi:10.3390/sym12030469

License

STRIKE-GOLDD is licensed under the GNU General Public License version 3 (GPLv3).

Funding

STRIKE-GOLDD has received funding from: Xunta de Galiza, I2C postdoctoral fellowship ED481B2014/133-0; Spanish Ministry of Economy and Competitiveness (MINECO) grant DPI2013-47100-C2-2-P; EPSRC projects EP/M002454/1 and EP/J012041/1; and the European Union Framework Programme for Research and Innovation (Horizon 2020, CanPathPro) under Grant 686282.