Initial Conditions¶
Oris reduces the state space prior to simulation by applying:
Media constraints
Calibration-based initial conditions
1. Media constraints¶
Media constraints depend on the experimental culture medium and are explicitly defined by the user in the configuration file (see Configuration). If the medium contains a ligand, activator, or repressor for a model node:
a dedicated input node is created,
a Boolean equation describing its effect is assempled,
and stable states in which that node is active are retained when required for downstream analyses.
2. Calibration-Based Initial Conditions¶
Gitsbe generates ensembles by selecting high-fitness models based on calibration data (see Helpers). Some calibration nodes may correspond to input nodes, which are unconstrained in Boolean logic.
To address this, Oris:
introduces an artificial regulator node that activates or inhibits the input node,
filters stable states to retain only those matching the calibration data.
This ensures consistency between experimental evidence and the states evaluated during downstream analyses.