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Lambda Switch

Lambda Switch. A Quantitative Analysis Group C: Simon Janssen Leroy de Leeuw Yuriy Savelyev Frenkel Smeijers. Overview. Research Questions Biological Model SpiCO Model SPiM Model SpiCO vs. SPiM Conclusions. Research Questions.

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Lambda Switch

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  1. Lambda Switch A Quantitative Analysis Group C: Simon Janssen Leroy de Leeuw Yuriy Savelyev Frenkel Smeijers

  2. Overview • Research Questions • Biological Model • SpiCO Model • SPiM Model • SpiCO vs. SPiM • Conclusions

  3. Research Questions • What is a λ switch and can we reproduce the switch in SpiCO? • How does SpiCO compare to SPiM?

  4. Biological Model • Two pathways of λinfected Escherichia coli bacterium: lysogeny and lytic growth

  5. Biological Model

  6. SpiCO Model • Numbers taken from experiments and literature • Includes cooperation, negative feedback, self inhibition • No external event  no induction  no lytic growth

  7. SpiCO Model 'cro' : object( with() profile('monomer' sum( send(channels#croDimerize sync 'dimer') receive(channels#croDimerize sync 0) ) ) profile('dimer' new(c:rates() sum( sequence( send(channels#proDock bind(c)) receive(c return(op)) send(op specCro) 'bound'(op) ) sequence( receive(channels#croDimerBreak sync) parallel( 'monomer' 'monomer' ) ) ) ) ) profile('bound'(op) send(op unbind 'dimer‘ ) ) ) ) )

  8. SpiCO Model Bindings of RNAP on PRM and PR

  9. SPiM Model • External event triggered

  10. π-calculus Lots of numbers and text No documentation π-calculus Graphical output Documentation SpiCO vs. SPiM

  11. Conclusions • The lysogeny state is very stable and usually needs an external event to change to the lytic growth • SpiCO is still under development  no documentation, no nice output • We are among the very first external users of SpiCO

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