Support the SED-ML for remaining biomodels

[luciansmith]

The temp-biomodels project has a lot of new SED-ML, and much of it is correctly interpreted by VCell, but there are some cases where there are breakdowns. Attached is a full list of every biomodel that doesn't run on VCell.

vcell_failures.csv

I'm also attaching the list of 22 models that don't run on Tellurium, because it's quite likely that those won't run on VCell either.

tellurium_failures.csv

Likely causes of many of the failures include:

• Support for steady state analyses (there are new KiSAO terms and tags)
• Support for changing an element value that didn't have a corresponding attribute.

[luciansmith]

Latest updates comparing VCell 7.5 to 7.6:

vcell_compare.csv

[luciansmith]

Update: anything in that spreadsheet marked 'running' eventually timed out and is now 'failed'. I'll leave it as-is for now, so it's clearer which failures were due to timeouts.

All the 'processing' runs are still processing. They might actually be stuck, but nothing has killed them, so they're still 'live'.

[luciansmith]

I changed my mind; it's possible one or two of them actually escaped the timeout somehow. Just in case, here's the actual updated spreadsheet:

vcell_compare.csv

[moraru]

@CodeByDrescher @jcschaff first order of business is to look at these (previously succeeding, now failing)

id  75_status   75_id   76_status   76_id
BIOMD0000001066 SUCCEEDED   66f1dacf19c07a4c8d029990    FAILED  66f1cfd919c07a4c8d021bfc
BIOMD0000001067 SUCCEEDED   66f1dad01f1841b171a1d7c6    FAILED  66f1cfdb88cf83b6bc85a01b
BIOMD0000001068 SUCCEEDED   66f1dad21f1841b171a1d7de    FAILED  66f1cfdd88cf83b6bc85a038
BIOMD0000001069 SUCCEEDED   66f1daf219c07a4c8d029afc    FAILED  66f1d0d888cf83b6bc85a308
BIOMD0000001070 SUCCEEDED   66f1daf81f1841b171a1d925    FAILED  66f1d0de19c07a4c8d021f6b
BIOMD0000001071 SUCCEEDED   66f1dafe19c07a4c8d029b21    FAILED  66f1d0df1f1841b171a16531
BIOMD0000001073 SUCCEEDED   66f1db0919c07a4c8d029b47    FAILED  66f1d0e219c07a4c8d021f95
BIOMD0000001074 SUCCEEDED   66f1db0a1f1841b171a1d967    FAILED  66f1d0e41f1841b171a16542
BIOMD0000001076 SUCCEEDED   66f1db0c19c07a4c8d029b4f    FAILED  66f1d0e788cf83b6bc85a333

[luciansmith]

The fact that those are all high-number models made me suspicious, and indeed, those seem to be biomodels with no actual SBML nor SED-ML in them. 'Failing' is probably the correct behavior.

[moraru]

@luciansmith you are correct - they are all ML stuff