About STRIKE-GOLDD

STRIKE-GOLDD is a MATLAB toolbox that analyses nonlinear models of ordinary differential equations. It performs a simultaneous assessment of:

• state observability,
• parameter structural local identifiability,
• unknown input observability.

Additional features include:

• search for the Lie symmetries that underlie non-observability and non-identifiability,
• automatic reparameterization to obtain a fully observable and identifiable model.

Since v4.1.0, it also provides tests for accessibility and controllability, by integrating the code of the NLcontrollability toolbox.

Most of these analyses are performed symbolically, and yield results that are valid for all values of the variables, except for a set of measure zero.

STRIKE-GOLDD was originally created by Alejandro F. Villaverde, afvillaverde@uvigo.gal. It now includes contributions from a number of collaborators.

Installation and requirements

STRIKE-GOLDD requires a MATLAB installation with the Symbolic Math Toolbox.

To use STRIKE-GOLDD you just need to:

1. download the code
2. open a MATLAB session
3. run install.m from the STRIKE-GOLDD directory
4. define the problem by editing options.m
5. run STRIKE_GOLDD.m or NLcontrollability.m, depending on the analysis

Alternatively, since v4.0 you can also use it as a Matlab app with a graphical interface:

1. download the code
2. open a MATLAB session
3. right click on MainApp.mlapp and press Run
4. define the problem, method, and options in the pop-up window
5. press the Run button in the pop-up window

More information can be found in the STRIKE-GOLDD manual.

Publications

Publication of the methodology (first version of 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

Extension for time-varying inputs (STRIKE-GOLDD 2):

Villaverde AF, Evans ND, Chappell MJ, Banga JR (2018). Input-dependent structural identifiability of nonlinear systems. IEEE Control Systems Letters 3(2):1–6, doi:10.1109/LCSYS.2018.2868608

Extension for unknown inputs; FISPO analysis (STRIKE-GOLDD 2.1):

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(156), doi:10.1098/rsif.2019.0043

Extension for finding Lie symmetries (STRIKE-GOLDD 2.1.6):

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

Extension for multi-experiment analysis and implementation of the ORC-DF algorithm (STRIKE-GOLDD 2.2):

Martínez N & Villaverde AF (2020). Nonlinear observability algorithms with known and unknown inputs: analysis and implementation. Mathematics 8(11), 1876, doi:10.3390/math8111876

Extension for automatic reparameterization, AutoRepar (STRIKE-GOLDD 3.0):

Massonis G, Banga JR, Villaverde AF (2021). AutoRepar: A method to obtain identifiable and observable reparameterizations of dynamic models with mechanistic insight. International Journal of Robust and Nonlinear Control, 33(9):5039-5057, doi:10.1002/rnc.5887

Extension for graphical interface & new algorithm, ProbObsTest (STRIKE-GOLDD 4.0):

Díaz-Seoane S, Rey Barreiro X, Villaverde AF (2023). STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability. Bioinformatics, 39(1), btac748

Description of the accessibility and controllability tests provided with the NLcontrollability tool (STRIKE-GOLDD 4.1):

Díaz-Seoane S, Barreiro Blas A, Villaverde AF (2023). Controllability and accessibility analysis of nonlinear biosystems. Computer Methods and Programs in Biomedicine, 242:107837

Disclaimer

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.