GSoC Week 7

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Hi,


Continuing the work on the SBML L3V2 issues, this week was also focused mainly on solving the SBML L3V2 issues occurring while testing the SBML Test Suite models. Here’s a quick summary of the weekly work report with the meeting summary:


  • In the last meeting, we mainly discussed the issues related to the SBML models with changing compartment size and on the implementation of the rateOf function. 

  • Mentors suggested that the current implementation of rateOf (getting the values from the changeRate array of SBMLinterpreter class) does not seem a good way instead should calculate the derivatives in the rateOf method itself. It passes for the current models with rateOf as they are quite simple but may fail on complex models.

  • We gave a lot of time of the week discussing the simulation of the SBML models with changing compartment size. We were not able to get the proper way how the SBML Test Suite calculated the results for these test cases. However this is not solved yet but you can give a look at the summary of the discussion of this issue at this link.

  • We discussed the issue "requested tolerances could not be achieved" and one of my mentors suggested that there may be some other problem like something is going on wrong in the sequence of processing the things. And while working on the issues, I found out that really the problem was something else.

  • The problem was that in some models of the SBML Test Suite, the conversion factors are given values using the initalAssignments while this was not considered by SBSCL. I added this to SBSCL and this solved the requested tolerance issue with some other failing models too. The commit can be found here.

  • We discussed building an observer on the results so that the output can be plotted until the time it is solved instead of waiting for the complete simulation. This has now been added to SBSCL and can be looked at this commit.

  • Also, I have made the tolerances of the simulator stricter by 0.01 which passed some more tests that failed due to small deviations.

  • The updateSpeciesConcentration method has now been updated in the SBMLinterpreter class. It is now separated into two methods namely updateSpeciesConcentrationByRateRule and updateSpeciesConcentrationByCompartmentChange describing their individual purposes rather than doing everything under the name of updateSpeciesCocentration. You can view the changes for this at this commit.

  • The delay property has been added to the SpeciesReference in SBSCL (Commit Link).

  • Also, I forgot to update the FBA tests when there was no feasible solution which was discussed quite before. This has now been fixed through this commit.

  • The column name 'Time' has now been updated to 'time' in SBSCL now


This is the complete information on the work I did last week. The complete updated work can be found at the testrunner branch of my forked repository. Also, PR #48 is made to the main SBSCL repository with all the updated code. Thanks for giving a read:)


Regards!
Location: Deesa, Gujarat, India

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