My final exam for the semester ended on the 27th of April, but the semester had not ended. I was busy with teaching assistant duties and projects till the 4th of May. A Google Hangouts call with Herbert, Leandro and Chris was held on the 2nd of May. It was nice to meet and talk face to face with them. I was requested to read the SBML Arrays specification and the “Efficient Analysis of SBML models using Arrays” paper to get a thorough understanding of what is required to be done for the rest of the summer. The student-mentor agreement form was filled up during the call.
Herbert provided a simple issue to solve to get more familiar with libRoadRunner codebase. libRoadRunner has configuration parameters and I had to add a new configuration parameter that allowed the user to decide whether steady state analysis should be carried out in the presence of events. The coding in itself did not take long but testing it took some time. Testing required building libRoadRunner and Tellurium from source. Tellurium was pulling an older version of rrPlugins during installation and was causing compatibility issues. rrPlugins had to be manually built and once that was done, testing was done against a few functions and the issue was solved.
I had a wonderful time at Singapore with my family from the 7th of May to the 14th. On returning, I followed up on the request to read the SBML Arrays specification and the paper.