SBML Simulation Feature Improvements

[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.

[umut-er]

I am currently implementing the parameter UI in this way (keeping with the convention of adding binding regions etc...)

However, since a lot of the models on the internet have a lot of parameters (20+ in many - or most - cases), maybe I should change the UI, putting "Parameters" as a header on top, and using a full row for each parameter. We can save a lot of space with that approach. This is not really an issue with local parameters, from what I have seen most people just use global parameters anyways.

We can make this change at any point in the future. I am focusing on the functionality for now.