Epic: public vcell models as SBML/Omex

[jcschaff]

Motivation

For those models which can be exported as SBML (or SBML Spatial), public and especially published VCell BioModels should be able to be successfully simulated in a reproducible way.

Completion Criteria

• export all BioModels as SBML/Omex to run in Biosimulations (if impossible)
  • Biomodels should round trip (math generation, math overrides, etc).
  • simulation results should agree with COPASI and Tellurium if applicable.
  • Simulations should run successfully in Biosimulations.
• For remaining public nonspatial models: document reason that SBML export cannot be accomplished.

Tasks

• Review simulator specs for model changes and observables #91
• Results are not correctly exported to CSV or HDF5 for VCML models #138
• Open zip files as omex files #140
• Round trip Disabled reactions to SBML (especially in SEDML context). #354
• math generation fails with global parameter J_r0 and Reaction(r0) #356
• CLI-python code for creating plots needs refactor to control color palette #366
• Math Generation Fails or is Incorrect when species have the same name as local parameters #490
• VCell does not support Sequential/Multi-sub-task Repeated Tasks  #498
• SBMLImporter consumes errors #515
• roundtrip fails due to math equivalency failure #522
• roundtrip fails due to various errors #523
• ExpressionUtils.getLinearFactor() should use SymbolTableEntries #551
• Importer brings in unused models #562
• CLI conversion should use saved math for validation #563
• 30 BMDB models fail to import with UNRESOLVED.initConc or UNRESOLVED.Size #803
• MathML parsing errors during BMDB import #804
• SedML export gives bad XPATH #890
• SEDML Exporter provides non-unique IDs  #891
• VCell Biosimulators CLI: stochastic simulation not working #912
• JobLogs for batch export no longer contain sufficient information to get round trip information. #944
• Support the SED-ML for remaining biomodels #972

Spatial Tasks

• VCell compliance with SBML spatial #211
• SBML export/import for CSG Geometry not working #423
• WIP: CSG round trip to SBML #424
• save PDE results as Vtk files

Model Processing Tasks

• Run all published models with status never ran #158
• improve ExpressionUtils.functionllyEquivalent() for expressions with discontinuities #430
• Species diffusion rates with value zero are not in constant list #475
• Membrane voltage namescoping inconsistent #506
• Indirect referencing of species concentrations fails math generation #642
• override resolver does not handle distributed volume fractions #718

VCML/Omex (out of scope for this PR)

• update importer and executor for VCML language format combine archives #719