Add Liu_IFACPapersOnLine2025

[m-philipps]

Yuhong's publication on oncolyte virus therapy in zebrafish has a model in PEtab format, at the moment in the preprint phase.

[EchoRLiu]

• model description: the models aim to describe the dynamics of oncolytic virus therapy (OVT) in zebrafish, focusing on tumor-virus interactions. The main working model is the age-of-infection model that incorporates delays in viral effects and individual variability.
• data description: the models use experimental data from a zebrafish study (Mealiea et al. (2021)), where tumor volumes were measured after injecting tumor cells and oncolytic viruses. The dataset includes daily tumor volume measurements for control and treated groups over five days.
• fitting and uncertainty analysis: fides was used and with the following hyperparameters
  • np.random.seed(500)
  • n_start = 5000
  • max_iter = 5000
  • hierarchical=False
    the optimization converges and most parameters are identifiable
• we fitted all parameters with bounds based on various publications

[EchoRLiu]

the subfolder individual-based contains a sub-model of age-of-infection model. The difference between the two is only the initial condition of the tumor cell number. In the individual-based model, each individual has its own parater $\xi$ to adjust how much tumor cells are homed, adjusting the individual initial condition of tumor cells.

[m-philipps]

The Journal's ISO abbreviation is IFAC-PapersOnLine but the resulting PEtab ID Liu_IFAC-PapersOnLine2025 can not be used as the SBML model id because of the -.

1. option: Use non-ISO journal abbreviation, e.g. IFACPapersOnLine
2. option: SBML model id does not match PEtab ID

[dweindl]

The Journal's ISO abbreviation is IFAC-PapersOnLine but the resulting PEtab ID Liu_IFAC-PapersOnLine2025 can not be used as the SBML model id because of the -.

1. option: Use non-ISO journal abbreviation, e.g. `IFACPapersOnLine`

2. option: SBML `model id` does not match PEtab ID

I'd go for option 1, or replace replace - by _.