Week 9: Wrapping Up Testing

-

Hi everyone,

As shared in the last blog that we have achieved a respectable result after running our algorithm against SBML Test Suite (Although, we are actively  looking into the remaining failed test cases). The focus has a little shifted from testing to documentation, community engagement, and preparing LSODA-Integrator for its final polished form.

We kicked off the week with a full-team meeting where I shared the latest SBML Test Suite results with the mentors. This marks a big milestone, as the LSODA-Integrator is now stable, accurate, and well integrated into SBSCL.

Our discussion revolved around the remaining 1% of failing cases — particularly those producing errors or no output. Dr. Dräger and Dr. Funahashi emphasized prioritizing these over tests with merely incorrect results. I explained my approach to event handling, delayed reactions, and fast reaction tags (described in detail in my Week 8 blog post).

Dr. Funahashi shared libSBMLsim as a possible resource to help investigate the remaining cases, and we also touched on the KiSAO number for LSODA-Integrator.

On the documentation side, I wrote a detailed a howToUse markdown guide for LSODA, with all the information a user will need to use the LSODA-Integrator in SBSCL in either way usage with SBML models or usage with direct ODE systems. Taichi and Arthur will try to reproduce and continue digging into the remaining failing cases from my earlier issue report.

We also planned some community outreach: more about that in next blog. Additionally, we’ll update the SBSCL Wikipedia page to reflect the new changes.

Thanks for reading.
Bye!

Comments

Post a Comment

Popular posts from this blog

Week 7: Events, Exhaustion and Evaluations

-
Image
Hi all, This week has probably been the toughest one yet. Not just mentally, but also in terms of hours spent chasing bugs that I had no idea about. I’ve logged over 50 hours on the project, and ironically, there’s not much “visible” progress to show. But deep down, I know this is part of the process, and what matters is that I’ve been able to get to the root of a tricky problem, more on that below. Updates From This Week Made the PR changes suggested by Dr. Dräger and Taichi. Ran the SBMLTestSuite using the wrapper program I wrote last week. I had already shared the test results with the team on Slack. Results? Mixed bag: Passed: ~85% of the test cases (Happy somewhat!) Wrong Output: ~12–13% Error: ~2% (No idea, why?) Results Map from SBMLTestRunner So naturally, I spent the entire week narrowing down those failed and wrong output cases. And guess what? I’ve finally figured out what's going wrong in most of the wrong output cases. The Issue: Event Timin...
Read more

My GSoC 2025 Journey Begins

-
Image
Hi,  I am Ayush Baranwal, a second-year engineering undergrad at Jawaharlal Nehru University, New Delhi, India. I am incredibly excited to share that I have been selected for the Google Summer of Code 2025 with the National Resource for Network Biology (NRNB) organization. This summer, I will be working on the project " Developing a highly efficient numerical ODE solver in Systems Biology Simulation Core Library (SBSCL). " I am incredibly thankful to my wonderful mentors, Prof. Dr. Andreas  Dräger , Dr. Akira Funahashi, Taichi Araki and Arthur Neumann, for their constant support and guidance throughout the proposal period. I am truly grateful for the trust they have put in me, and I am fully committed to making this project a success. What This Blog Series is About This blog series will document my journey throughout GSoC. Prof.  Dräger  suggested keeping a public log during our first meeting post-selection—more on that in the next blog! The goal is to keep my work ...
Read more

Week 1: Coding Period Begins

-
Hi everyone, The official coding period has now begun, and I've diving deeper into the LSODA internals. Continuing from the last blog post, I focused primarily on refactoring helper methods within the LSODA package, while also  setting the foundation for a robust and modular design.   After reading some of the core literature on LSODA, I decided to examine the libLSODA codebase—the C library of LSODA translated from its original Fortran implementation in ODEPACK. My first step was to outline the overall program flow of the LSODA algorithm , which helped me visualize where and how different components fit together.   Upon exploring the main lsoda function, I chose to start by implementing and refining the helper functions , as they form the building blocks of the algorithm. I thoroughly reviewed the SBSCL LSODA implementation so far and identified areas for improvement. Here's a more detailed  explanation of my work ( PR ),  followed by wha...
Read more