GSoC 2025: Developing a highly efficient numerical ODE solver in SBSCL

Hi all, Okay, Continuing our story from last blog. So, after spending the past week chasing down the issue with SBML Test Suite failures (which I elaborated on in my last blog post ), I finally got a breakthrough that brought us closer to a robust and reliable LSODA integration in SBSCL. Revisiting the SBML Test Suite Challenges Previously, around 12% of the tests were failing and 2% were throwing outright errors. After narrowing the root cause down to event handling discrepancies, I spent this entire week diving deeper into tackling this challenge. Dr. Dräger shared a fantastic resource ( link ), which not only confirmed my theory but also revealed that previous developers had faced similar problems while implementing the Rosenbrock solver in SBSCL. It turns out that precise event time detection is a non-trivial challenge when dealing with SBML models. When events are triggered between timepoints (say at tτ , which lies between tτ−1 and tτ+1 ), evaluating events only at thos...

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...

Hello again! Week 6 of my GSoC 2025 journey has been all about refinement, feedback, and forward momentum . I finally opened my long-standing pull request with the work done over the past three weeks. Here are more details around it. The Pull Request On July 7th, 2025 , I submitted a pull request that encapsulated all the major changes and improvements I’ve worked on since Week 3. This included: The updated LSODA package A clean interface supporting both SBML input and direct ODEs Multiple system-level tests for validation Detailed exception handling for edge cases Detailed method-level docstrings  Once opened, the PR served as a starting point for deeper discussions with my mentors — not just about what’s working, but how things can be made even better. SBMLTestSuite: Building the Test Bridge As part of verifying LSODA’s reliability in a broader context, I started my work on testing the solver against the  SBML Test Suite . I read the documentation and l...

 Hi readers, This week marked a subtle shift in focus — from writing core components to understanding and aligning LSODA with SBSCL’s broader infrastructure. It wasn’t my most productive week in terms of code commits, but it was certainly rich in learning and architectural clarity . Understanding SBML The week began with me diving deep into SBML (Systems Biology Markup Language) — not just from a theoretical perspective, but also to understand how it flows through SBSCL. I read the document shared by Dr. Funahashi  (translated it to English from Japanese first, thanks to Google Translate). I also watched the  video shared by Dr. Dräger . Both were really helpful. I explored SBMLSimulator , which provided concrete examples of how SBML models are parsed and simulated. Thanks to these resources, I finally got a clear picture of how: SBMLInterpreter   parses the SBML file and constructs the mathematical model. Multitable stores the simulation results and pr...

Hi readers, It’s week 4 of my GSoC journey, and this week was all about building bridges — between code and interface ,   and initial testing . As I move from core algorithm development into integration, things are getting both more exciting and more layered. What I did this week? After completing the lsoda driver function last week, I began working on the integration mechanism — i.e., how users will interact with the solver, and how models will be parsed, solved, and tested. Here’s what I’ve done so far: I implemented the computeChange abstract method which is the go to method for AbstractDESolver for solving the ODE systems. It is the single most important method for the integration mechanism. I created a new test class LSODASystemTest , specifically to validate how LSODA handles various   ODE systems  and error scenarios in an end-to-end manner. I’ve designed the LSODA solver to work in two different modes : Direct ODE system input – where users can d...