8000 SBML Simulation Feature Improvements · Issue #755 · iVis-at-Bilkent/newt · GitHub
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SBML Simulation Feature Improvements #755
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@umut-er

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@umut-er

Now that the SBML Simulation branch is live on our development server, I would like to summarize what needs to be added / improved.

  • 1. Support for SBML Parameters and SBML Local Parameters (both in the UI and import / export). This is especially important from a testing perspective, since it is extremely rare to find an SBML model on the internet with no parameters.
  • 2. There is a known bug where after importing an SBML file with kinetic data, we can't see the kinetic data in the UI. However, simulation still works.
  • 3. The simulation feature should work out of the box without setting any kinetic data for reactions. For that reason, the kinetic data should default to 0.
  • 4. The simulation backend allows us to generate data (over time) for the amount of a species, the concentration of a species, the speed of change of a species. Currently, we only show the user the concentration over time. We can give them the choice.
  • 5. In the simulation literature, there are various terms like Metabolic Control Analysis, Stochastic Simulation, Steady State Analysis... I don't know exactly what these are, or for what purpose these are useful, or if we are interested in implementing these.
  • 6. SBML has a number of other features that we can look to implement. They are listed in the SBML Specs under section 4. We currently implement Compartments, Species and Reactions.
  • 7. There is a known bug concerning the parameters, they are not properly discarded when we load another file on top of an existing one.
  • 8. Prepare a testing environment to check against the SBML Test Suite, for the implemented features.

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