Some species (species not involved in rate equations?) aren't recorded

[jonrkarr]

Since there doesn't appear to be a way to record the values of non-constant parameters (e.g., needed for some plots in BioModels), I tried to see if I could use an assignment rule to record the values of non-constant parameters (i.e., assign the value of a parameter to a species).

Example: dNFAT (parameter) and dNFAT_species (species) in BIOMD678.xml.txt.

However, PySCeS didn't record the value of dNFAT_species. One possible hint I see is

Info: "dNFAT_species" has been initialised but does not occur in a rate equation

I have two questions:

• Is there a direct way to record the values of non-constant parameters?
• Is there a way to record the values of such species set via assignment rules? i.e., is there something else I can do to trigger PySCeS to record their values?

[jmrohwer]

This has now been fixed in Release 1.0.2. Assignment rules are tracked by default in a simulation with CVODE, and the values are available via mod.data_sim.getXData(). Refer to https://pyscesdocs.readthedocs.io/en/latest/userguide_doc.html#simulation-results

The change was implemented in https://github.com/PySCeS/pysces/pull/77/commits/8ebbcb326d205e5818e4a7a350eb645c11d83c0e with additional fixes in https://github.com/PySCeS/pysces/pull/77/commits/e9c4444ae2b525cfb32c1e0192eea4b3e20577fd.