Sunday, June 28, 2026

Thanks AI

Github Copilot is making the Human Body Simulation project so much more interesting for me. I currently have Claude 4.8 converting the old WholeCell fork I have at https://github.com/navoj/WholeCell to Squeak Smalltalk as a single cohesive image file: https://github.com/jtrujil43/SqueakWholeCell It churns in the Matlab code in little batches but it already makes a nice little dummy simulation on various aspects of mycoplasma genitalium metabolism and growth. I now know there is a newer version of WholeCell now ported to Python and some standardized model library for large systems. I have not tried getting that code to work for me yet. I'll try to focus on the old Matlab version because I can compare to the newer way of doing things. I also learned that eCell can't simulate a whole cell. Its more or a toolkit for modeling parts of the biological process.

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