COMBINE Notebooks GSoC 2022 Project

As I progress in the project, it keeps getting more challenging. Thankfully, I have my mentor Dr.  König  to guide me whenever I'm stuck. This week was focused on creating tests for validating the repressilator models using tox. I'm facing an issue with 'mypy' and hope to resolve it in today's meeting. Next, I worked on the antimony model for the repressilator. It's still going on, and I'm facing a peculiar issue: while all packages are installed in the virtual environment, the program still throws errors that packages are not found surprisingly.  Looking forward to today's meeting and resolving these issues asap.

I introduced myself to the COMBINE community over slack and google groups and received positive interaction from a few community members.  Following a successful start to my GSoC project, I have been having regular weekly meetings with my mentor Dr. Matthias  K ö nig .  I completed the script for libsbml for repressilator: added compartments, species, parameters, assignment rules and reactions (which are basically kinetic laws) and committed the code to Github. The snapshot below shows an output of what the running example looks like. In addition, I started working on using sbmlutils for repressilators. Dr. K ö nig's previous project  https://sbml4humans.de/   has been particularly useful in displaying the complex repressilator in an easy-to-understand format. I have created compartments, species, parameters, assignment rules and reactions similar to libsbml, however, am currently running into issues creating reactants, products, and modifiers. I'll be discussing this with Dr.

This blog post has been long overdue. I received my official acceptance email into the Google Summer of Code 2022 on May 20, 2022. It was a joyous moment to know that all the hard work preparing for it had finally paid off. I'll be spending my summer working on "Creating Jupyter Notebooks Showcasing COMBINE Standards" under the National Resource for Network Biology organization. Dr. König gave his best compliments and we charted out the plan for the next few weeks. I started working on the first repressilator notebook: using libsbml.  ' I created compartments, species, and kinetic laws showcasing libSBML using repressilator. This week, I'll be adding more features to it and doing a bunch of other stuff. Stay tuned for the next post!