In summary, AutoMerge can be thought of as a preliminary step, which solves simple merging issues while combining models; and, the modeler can then manually interfere and make changes to the composed model to ensure correctness.
The composed model is used to study the benefits of joint development and production planning in comparison to planning these two phases of the project separately.
However, this discrepancy in the sets of variables, x η and x ε, comes at the cost of additional work required to formulate the composed model, combining the reversible and irreversible dynamics.
The composition of all timing models generated from the tasks from the per-task analysis yields a complete system model which is also safe, because the composed model over-approximates the possible interference between the tasks.
As the composed model follows standard SBML specifications, visualization interface works on the composed model on the fly.
All tabs are provided for the composed model as well, after the merging is complete.
In particular, the composed model contains all information of the submodels used in the composition process without any redundancies, although the information related to the relationship between elements of the composed model and the submodel is lost.
reaction2 elements will not be merged in the composed model, but their original ids cannot be kept in the composed model either since SBML defines id attribute as a unique identifier for each model.
When two models are combined, the simulation interface is available to simulate the composed model without any additional steps.
2. Otherwise, do not merge the compartments, and add both compartments as separate compartments into the composed model definition.
