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