Logan Drescher

Epic: MVP for Spring SaLaD in VCell

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Develop a minimal viable product (MVP) for integration of SpringSalad into VCell. ### Motivation VCell supports agent-based rule based simulations using NFSim, and non-rule-based particle simulations using Smoldyn. SpringSalad is...

According to the sedml spec, when a RepeatedTask specifies a range attribute, it's purpose is to be used via the shorthand `range` in the math portion of the change's `setValue`...

Reproduced with SASCO model through a docker container and VCell published models `VCDB_101962320` and `VCDB_101981216`. When running an sbml-omex based simulation that calls upon FiniteVolume Solver, there's a chance a...

Testing Framework encounteres a RPC DataAccessException

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The following error occurred trying to use the testing framework: 

### 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**...

Spatial simulations can produce HDF5, but if it's not produced in the biosimulation's style format, then our 3rd party users can use our spatial solvers. Note that this is blocked...

BNGL import erroneously scales initial conditions by 2e-5

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When BNGL is imported and option "Molecules" is selected, all initial counts are multiplied by 2e-5. No scaling (everything is OK) when "Concentration" option is selected.

When a rule-based model is saved (or flattened to generate a network), the step of generating observables takes disproportionally long time.