GSoC Week 12

Another great week and exciting news that I passed the second evaluations successfully😊. Again extreme thanks to the mentors ready to help and guide me at any moment. Last week, I mainly worked on refactoring the classes and enabling the feature of seeing processed results in realtime rather than waiting for complete simulation. Here’s the summary of the work done with updates from the weekly meeting:


  • We discussed on the newly added class EquationSystem, which now has all the initializations from the SBMLinterpreter only left with the processing things. This now separates the things from SBMLinterpreter, which now makes it look more transparent and better than before.

  • One of the mentors suggested refactoring various variables, comments, and methods in EquationSystem class more explanatory and proper as they didn’t seem to go better, which has now been updated.

  • We also decided to make a PR with all the stochastic simulation updates (fern branch in forked repo), and it is now open at this link.

  • After the reviews in the PR, the CSVImporter class has been completely updated. Before it did not had a proper implementation of reading CSV file to the MultiTable which has now been fixed, you can see the updated CSVImporter here.

  • The SBMLTestSuiteRunnerWrapper class, which simulates the model and updates the result in the CSV format which is used by SBML Test Runner to plot the results and distances, has been refactored with the code completely separated in different methods. The complete changes are made through the linked commit.

  • PropertyChangeListener has been added to the AbstractDESSolver, which now enables SBSCL to get a new feature🎉 for getting the results as soon as they are processed instead of waiting for the simulation to complete. This is now added to the SimulatorExample where the results are logged at each time step while simulating. Here's a gif showing the processed results at each timestep.


  • After this, we decided to refactor FERN to use the SBSCL classes, which makes SBSCL even better with the EquationSystem and SBMLinterpreter as central classes. I worked on understanding how FERN is working with the classes and has some issues which I will be discussing in my next blog so, stay tuned for that😉!


These were the main work updates this week with a new feature to SBSCL. The updated work is present at the fern branch at my forked repository. 


Regards!


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