Cell evolution game - basic interface

Today I started to make a game that I've been thinking about for a quite a while now (I mention it here). The general idea is that you play as a single-celled microbe which evolves ever more complex metabolic and regulatory systems as it moves to ever more challenging environments.

Adding ribosomes to my cell simulation

This is a description of some work I did on an older version of my cell simulation.

So far, the main adaptation that cells in my simulations have evolved has been an increase in of gene copy number. Such adaptations are unsurprising given that it's the only way cells can alter the relative amounts of each protein. In my final simulation I want to allow cells to alter gene expression using transcription factors to control rates of transcription (and thus translation).

Macrophage chemotaxis

I updated my macrophage simulation to use my Python particle module, which I describe here. I was pleased how straight forward it was to effectively re-create my previous simulation from scratch using a few simple commands. There are a few changes I'd like to make so creating new simulations will be even quicker in future.


Cell Simulation

A simulation of single celled organisms and their evolution with the focus on metabolic and regulatory pathways.

Short cell simulation update

Once again I’ve been neglecting my blog. I think I have a good excuse, which is that I was writing my thesis. That hasn’t stopped me from doing the odd spot of programming however. I’ve made some progress with my microbe simulation, notably, making a GUI to visualise where on the DNA various proteins bind. I have also started a separate microbe simulation, which is more of a game to see who can evolve the fittest microbe in the primordial soup. The game elements are all there, but the program is ugly and the game limited; a bit more work is required to make it fun to play.

Macrophage simulation

While discussing some of my programming projects in the pub, I mentioned using biological approaches to creating a Artificial Intelligence to play Go. I was initially thinking of evolving solutions, but the conversation gradually moved into a biological analogy for Go: two teams of macrophages, one black, one white, trying to engulf one another.