eighty-twenty

Notes:

• The central dogma has information flowing in one direction only. This fits the Darwinian view of the world; if information were able to flow back from proteins to the genetic (hereditary) material, we would have a more Lamarckian system. It turns out, of course, that there is information flow in the reverse direction — promoters, operons, regulatory sequences, signalling molecules etc. — but it only seldom (never?) modifies the genetic material in a heritable way.
• Michaelis-Menten equations are used to model cooperative factors in transcription.
• “Simulate Biologists! Not Biology!!” - simulate biological reasoning. Faithful simulation of the actual biological system not required.
• “Simpathica is a modular system”
• There’s a canonical form for each described reaction system.
• An example given is glycolysis. It’s written as a composition of building blocks. The modular nature of the simulation system means you can build libraries of modules.
• It does ODEs and (maybe also) PDEs
• The experiments on artificial regulatory circuits didn’t match the simulation - lots of effects need to be taken into account, e.g. RNAP run-on, …
• Very cool “story generation” technique - ask questions about a whole bunch of variations on a model - it tells you in natural language about the results! (Also can query in natural language)