Known limitations

Always select all simulations associated with a Monad

Anytime a group of simulation replicates (a Monad in PhysiCellModelManager.jl internals) is requested, all simulations in that group are used, regardless of the value of n_replicates.

Initial conditions not loaded when launching PhysiCell Studio for a simulation.

When launching PhysiCell Studio from PhysiCellModelManager.jl, the initial conditions (cells and substrates) are not loaded.

Limited intracellular models

Currently only supports ODE intracellular models (using libRoadRunner). Does not support MaBoSS or dFBA.

Compiled executables are not keyed to the machine that built them

PCMM names each executable for the PhysiCell version it was built against, so it recompiles when that version changes. It does not track the operating system, architecture, or compiler flags used. Move a data/ folder to a machine those differ on and PCMM will reuse an executable that cannot run there. Pass force_recompile=true to run once on the new machine, or delete the pcmm_build/ folders under data/inputs/custom_codes/.