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.

Can't simulate the human body without music!

If you like classical music then check out my debut single:

https://sweetjehosavan.bandzoogle.com/

Human simulation in science fiction

I just read the short story Painwise that described how human body simulation was being utilized to deal with the future world’s medical problems. They covered some interesting problems with the idea of using simulation to create the perfect drugs. Every person’s DNA is too unique to cover in a simulation. Only generic genetic profiles can be used and a person’s epigentic contwnt will also be an unknown factor affecting possible side effects with drug design. 

Update

I have dedicated a pair of notebooks for the cause. I'm still learning many things. Need to start filling up those notebooks and posting what I learn to this blog.

Check out Notebook Stories for a chance to win Monologue Notebooks!

What is this blog all about?

This blog will be the main interface to the Human Body Simulation Project. All software development, modeling, and simulation results will be presented here. Anyone is free to comment on our progress as we strive to fully characterize the human body for future researchers to use. Such an ambitious project,we believe, is best done in the spirit of the free software movement. Volunteers will learn how to create models, and our computing cluster will run batch jobs to generate results for our community to utilize.

The project is still in its infancy, but for starters we are using the Whole Cell (http://www.wholecell.org/) as our foundation. The goal of this project is to provide the simplest possible interface to quickly get biology work done in silico for anyone who is interested. The software will be tested for errors and ported to C++ to enhance its portability to as many platforms as possible. We have a heterogeneous cluster with various operating systems and hardware platforms which will be used to test portability.

We hope you are excited to help us with this project. Its very ambitious but with the global community's help we can make amazing things happen!