Artificial Biochemistry

Lectures (All: PDF.zip 16M)

• One: Biology
  • Course Intro
  • Abstract Machines of Systems Biology
  • Model Construction and Validation
  • Probability Distributions (and SPiM intro)
• Two: Stochastics
  • Stochastic Communicating Automata
    • Case Studies: Epidemics
    • Case Studies: MHC Class I Flytrap
  • Stochastic Collectives
    • Case Studies: Repressilator
  • Varieties of Stochastic Calculi
• Three: Chemistry
  • Chemistry and Processes
    • Case Studies: Scaling Reactions
    • Case Studies: ERK Pathway
  • From Processes to ODEs
    • Case Studies: Epidemics ODE
    • Case Studies: Groupies ODE
• Four: Biochemistry
  • Complexation
  • PolyAutomata
    • Case Studies: MapK Cascade
  • Monopolin Circuits
    • Case Studies: Inverter ODE
  • Dipolin Circuits
    • Case Studies: Franois and Hakim
• Five: Networks and Transport
  • Gene Networks
  • Bitonal Membrane Systems
  • Brane Calculi
  • Conclusions

Tools

• SPiM (Caml / Unix-Win-Mac / CommandLine)
• SPiM Player (F#-VS / .NET / GUI)