20080620 Formal systems/synthetic biology modelling re-engineered
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20080620 Formal systems/synthetic biology modelling re-engineered
- 1. formal systems / synthetic biology modelling re-engineered Jonathan Blakes 1 st year PhD student 2008-06-20
- 5. formalisms bacteria environment bacteria Petri nets P systems π -calculus reactions interactions lasI S 100 [ lasI ] -> [ lasI + LasI ] [ LasI + S ] -> [ LasI + 3OC12 ] [ 3OC12 ] -> 3OC12 [ ] LasR rhlR 3OC12 [ ] -> [ 3OC12 ] [ LasR+3OC12 ] -> [ LasR.3OC12 ] [ LasR.3OC12 + LasR.3OC12 ] -> [ LasR.3OC12 2 ] [ LasR.3OC12 2 + rlhR ] -> [ LasR.3OC122 + rlhR ] 3OC12 50
- 7. biological mapping Petri nets P systems π -calculus molecular species place symbol symbol molecule token object process population of molecules marking of net multiset processes reactions transitions rewriting rules communication
- 8. properties Petri nets P systems π -calculus discrete (mechanistic) concurrent non-deterministic ( uniform time steps ) stochastic variants ( realistic time steps ) SPN MCG, DPP S π compartments distinct places: X nucleus X cytoplasm membranes S π @ BioAmbients Brane calculi
- 9. why is stochasticity important? Gilmore S. A Beginner's Guide to Stochastic Simulation . Uni. Edinburgh, Systems Biology Club talk, 16/11/2005
- 17. a faithful approximation Gilmore S. “ Beginner’s Guide to Stochastic Simulation” University of Edinburgh Systems Biology Club talk 16/11/05
- 21. affect of membrane structure v = v – v’ v v’
- 22. dynamic volumes v 2v cells grow
- 23. dynamic volumes v cells divide
- 24. dynamic volumes cells divide v/2 v/2
Editor's Notes
- bipartite digraph, place and transition nodes
- stochastic methods associate an experimental determined rate with each reaction
- Circadian clock actually a consequence of continuous quantities
- A critical reaction is a reaction with positive propensity function such that a small number of firings is currently left before exhausting one of its reactants. All the other reactions are named, instead, noncritical reactions.
- if our approach implements tau-leaping it really can’t work any differently than in DPP, therefore the two approaches are united
- shortage of rate constants
- relative or absolute heat measures
- T-invariants can be used to analyse can average heat over simulation intervals to see which reactions were most likely in interval comparing averages for different intervals could highlight unknown switches in behaviour theoretically infinite number of strings