Example ODE model graphs and formulas
ode_models.RdA list of example "graphs" and specie formulas that can be passed to
EZDynamics or SimulateDynamics, and that are used under the hood
by EZSimulate to facilitate simulations of ODE models.
Format
ode_models
A list with 6 elements
- nuc2cyto
Simplest model of nuclear and cytoplasmic RNA dynamics: 0 -> N -> C -> 0
- preRNA
Simplest model of pre-RNA and mature RNA dynamics: 0 -> P -> M -> 0
- preRNAwithPdeg
Same as preRNA, but now pre-RNA can also degrade.
- nuc2cytowithNdeg
Same as nuc2cyto, but now nuclear RNA can also degrade.
- subtlseq
Subcellular TimeLapse-seq model, similar to that described in Ietswaart et al., 2024. Simplest model discussed there, lacking nuclear degradation: 0 -> CH -> NP -> CY -> PL -> 0, and CY can also degrade.
- nuc2cytowithpreRNA
Combination of nuc2cyto and preRNA where preRNA is first synthesized, then either processed or exported to the cytoplasm. Processing can also occur in the cytoplasm, and mature nuclear RNA can be exported to the cytoplasm. Only mature RNA degrades.
Each element of list has two items
- graph
Matrix representation of ODE system graph.
- formulas
Formula objects relating measured species to modeled species.