GSoC Week 8

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Last week, I successfully passed the first evaluations and was extremely happy to get the mail saying, ‘Congratulations! You have passed the first evaluation’. A big thanks to the mentors, especially Andreas and Matthias, for helping me throughout just from the beginning.


Now, coming to the work done last week with the updates from the weekly meeting.

  • There was an issue in GLPKSolver that its instance was not deleted after its usage, which gave a memory allocation error. This was an issue with the SCPSolver library, which we are using as a linear programming interface to solve FBC models. I resolved the error currently by making a temporary copy of the GLPKSolver in SBSCL with deleting the instance of GlpkSolver after its usage, which solved the issue.

  • I also mailed Dr. Hannes Planatscher, the developer of SCPSolver, to resolve this issue in SCPSolver. He confirmed to solve this in the coming months till that we decided to keep the temporary class as a workaround for SBSCL. This issue also failed the Travis CI build, which now runs fine. You can view the workaround class at this commit.

  • The new array failedTests is added to the SBMLTestSuiteTest class, which now keeps track of all the failed SBML Test Suite tests with the comments, if any, for particular test cases. And I skipped that tests temporarily in the test class to successfully pass the Travis build in the main repository.

  • There were few failing test cases from SBML Test Suite, which were having a negative stoichiometry for the SBML L1V2 models, which is not allowable. I filed an issue #70 for that in the SBML Test Suite repository, and models were removed from SBML Test Suite. This allowed that failing test to pass now. Also, the same issue is reported in the libsbml now.

  • There was a small issue (just single line change) while solving the SBML models having fast reactions that failed around 19 tests. This has been fixed now through this commit.

  • After making these changes, we finally merged the PR #48 containing all the work done until the first evaluations to the main SBSCL repository.

  • With this, I also solved the issue of the SBML models with compartment sizes this week. We had quite a long discussion for this issue (also shared the discussion in the last blog) but finally got a proper working solution. I updated the method of calculating the rule value also to consider the compartment's rate rules when species are dependent on them (Got this idea after the suggestion from Lucian Smith in the GitHub issue #50). The changes made to solve this issue can be found here.


This was the complete description of the work done this week and with this most of the models from the SBML Test Suite now pass the tests. To be precise, after this week, 125 models out of 1809 are failing. These failing models also include 90 comp models that are having issues due to JSBML. In the remaining SBML models, the significant issues are in the SBML models having events with delays and in interpreting the Algebraic rules as Assignment rules.


The complete work of the first evaluations can now be found at the main SBSCL repository linked here. The updated code after the first evaluations can be found at the testrunner branch of my forked repository.


Regards!
Location: Deesa, Gujarat, India

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