vliviu / strike-goldd

A MATLAB toolbox for structural identifiability and observability analysis of nonlinear models

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 invertibility (supported since v2.1.1).

The analysis is performed symbolically, and yields results that are valid for all values of the variables, except for a set of measure zero. More information is available at the STRIKE-GOLDD website.

STRIKE-GOLDD was created by Alejandro F. Villaverde, [e-mail].

Installation and requirements

STRIKE-GOLDD requires a MATLAB installation with the Symbolic toolbox. Additionally, if one wishes to use optimization-based decomposition, the MATLAB version of the MEIGO toolbox is required.

To use STRIKE-GOLDD you just need to:

1. download the code
2. open a MATLAB session
3. run install from the STRIKE-GOLDD directory
4. define the problem by editing options.m
5. run STRIKE-GOLDD

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 (2019). 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 (STRIKE-GOLDD 3.0):

Massonis G, Banga JR, Villaverde AF (2020). Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. arXiv, arXiv:2012.09826 [eess.SY]

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/.