This repository provides the relevant codes, scripts and data to perform structural identifiability analysis (SIA) and practical identifiability analysis (PIA) for bioengineering models.

The SIA is performed in MATHEMATICA which requires a license. A trial version of MATHEMATICA can be downloaded from https://www.wolfram.com/mathematica/trial/. In addition to this the Exact Arithmetic Rank (EAR) tool which is used in MATHEMATICA can be requested from: identifiabilityanalysis@fcc.chalmers.se. Although the Taylor series approach in this repository is performed using MATHEMATICA, a PDF copy is also provided in order to enable users to view the analysis and utilise their preferred symbolic software to perform the Taylor series approach.

The PIA is performed in MATLAB, using the Data2Dynamics tool: https://github.com/Data2Dynamics/d2d/wiki/Installation. MATLAB also requires a license however, a trial version can be downloaded from https://uk.mathworks.com/campaigns/products/trials.html.

References for all the models

Model 1: Krantz M, Legen J, Gao Y, Zoschke R, Schmitz-Linneweber C, Klipp E. Modeling indicates degradation of mrna and protein as a potential regulation mechanisms during cold acclimation. Journal of Plant Research. 2021;134(4):873–83. doi:10.1007/s10265-021-01294-4

Model 2: Yongky A, Lee J, Le T, Mulukutla BC, Daoutidis P, Hu W-S. Mechanism for multiplicity of steady states with distinct cell concentration in continuous culture of mammalian cells. Biotechnology and Bioengineering. 2015;112(7):1437–45. doi:10.1002/bit.25566

Model 3: Glen KE, Cheeseman EA, Stacey AJ, Thomas RJ. A mechanistic model of erythroblast growth inhibition providing a framework for optimisation of cell therapy manufacturing. Biochemical Engineering Journal. 2018;133:28–38. doi:10.1016/j.bej.2018.01.033