GSoC 2020: Simulation of Systems Biology Models in Java

Hi, We had our last meeting of the community bonding period last week on 26th May. As always, it was again great meeting the mentors. We discussed further on the issues of running the SBMLTestSuite tests and some other points with this. And, now the community bonding period has ended, and many new changes have been added to SBSCL. Here’s the summary of the work done in a week with the meeting: Continuing the discussion about the SBMLTestSuite tests from my last blog, we decided to compare the plots of the SBSCL simulator results with the pre-defined results and check the distances between them. For this, we decided to use the SBML Test Runner , a standalone desktop application with a GUI for controlling SBML-compatible applications and making them run test cases from the SBML Test Suite . I worked on this and made a wrapper for SBML Test Runner to run the tests using the SBSCL simulator. The documentation for how to work with SBML Test Runner has also been added to the INSTALL.md file ...

Hi, Last week on the 19th of May, I met with the mentors again for the second time on Zoom. However, one of my primary mentors, Andreas Dräger, was meeting for the first time as he was unable to attend the first meeting due to the Ph.D. defense. It was great meeting him after a long discussion on the mails. Now, here's the summary of the meeting with the weekly work done. Mentors confirmed in the meeting that the comp tests' issues were due to the CompFlatteningConverter class of JSBML. So, we decided to skip the tests currently and move forward until the issue gets solved in the JSBML repository. Matthias made an issue for the same in the SBSCL repository (issue #36 ) as well as the JSBML repository (JSBML issue #213 ). And, PR #37 was merged in the SBSCL repository with skipping the comp tests. Also, build with oracle JDK 11 was added to Travis CI. Then, we discussed that I should start working on the first milestone for the project, i.e., upgrading SBSCL to support SBML Lev...

Hi, Last week on the 12th of May, I had my first online meeting with my mentors on Google Hangouts. It was a fantastic experience meeting them. We discussed how to start with the project. Here’s the summary of the meeting and the weekly work done: There was a discussion for understanding the overall structure of the project. The most important suggestion from mentors was to write tests for any of the new features added. It confirms the results of the code and also makes it easy for the reviewers. We decided to start working on the small issues currently present in the codebase. The first issue discussed to solve was the Travis CI failing issue ( #34 ) for SBSCL. It was just upgrading Travis to OpenJDK11 and OracleJDK11 from the OracleJDK8 (which requires a license and all). I resolved the issue, but again, Travis failed with some issues due to a class from JSBML ( #36 ), which will be solved once JSBML updates it (currently, those specific tests are skipped from Travis). Also, I update...