Epic: MVP for Spring SaLaD in VCell

[CodeByDrescher]

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 an agent based simulation solver which uses a coarse-grained spatial representation of molecules. SpringSalad was developed independently of vcell, but can and should be integrated into vcell as another Application type, and the solver and simulation resutls should also be integrated.

Completion Criteria

• SpringSalad Math model and Langevin solver should be fully integrated (modeling, computation, data processing)
• SpringSalad BioModel applications should be supported.

Tasks

• [x] https://github.com/cam-center/LangevinNoVis01/issues/2
• [x] #1079
• [x] MathModel (and math description) with local for Langevin solver with minimally viable data analysis
• [x] #1135
• [x] BioModel application for SpringSalad.
• [x] #977
• [ ] #1480
• [x] #1481
• [ ] #1482
• [ ] #1508
• [ ] #1509

Future work (out of scope)

• [ ] support for curved surfaces
• [ ] support for parallelization

[danv61]

I was able to create a Springsalad math model from a biomodel, ran the Langevin solver on the input data created from it and display some results.