GSoC 2020: Simulation of Systems Biology Models in Java

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...

Hi, I am Hemil Panchiwala, 2nd year CSE student at the Indian Institute of Technology, Roorkee, India. I am incredibly excited to share that I was selected in the Google Summer of Code (GSoC) this year with the National Resource for Network Biology (NRNB) as a mentoring organization. I will be working on the project " Simulation of system biology models in Java: support for new features " in this program. I am incredibly thankful to the wonderful mentors, namely Dr. Andreas Dräger , Dr. Matthias König , Mykola Zakharchuk, and Shalin Shah , who helped me to get selected and will guide me throughout this project. This blog series is dedicated mainly to share my progress for the project. The official coding period starts from 1st June, and the community bonding period has currently begun. In this period, I will be exploring the codebase with solving some small issues and will discuss the implementation details with the mentors and finalize them. What is NRNB? The aim of the ...