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Epic: fix remaining issues with biosimulators_vcell for spatial simulations

Open CodeByDrescher opened this issue 2 years ago • 0 comments

Motivation

A highlight of the VCell solvers is the inclusion of spatial solvers. An important goal for us is allowing 3rd party usage of these solvers through the biosimulators_vcell container. This container is used when running vcell simulations on the run.biosimulations.org service. However, with missing infrastructure on both VCell's and BioSimulators' codebases, there is still extra work to do even after implementing non-spatial support.

Completion Criteria

  • BioSimulations must update their SED-ML report style specification to specifically address spatial simulations, while adhering to both SED-ML specifications while still delivering the same amount of information that is expected in a nonspatial simulation
  • the biosimulators_vcell container must pass new and specific spatial acceptance tests in BSTS (Biosimulators Test Suite)
  • the biosimulators_vcell container must run those vcell published biomodels which are to be deployed as biosimulations.org projects with success on run.biosimulations.org.

Tasks

  • [ ] #1048
  • [ ] #1068

CodeByDrescher avatar Dec 05 '23 13:12 CodeByDrescher