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Heat shock response & Petri-net

Computational Biomodelling Lab. Department of Information Technologies, Åbo Akademi University, 20520 Turku, Finland. Heat shock response & Petri-net. The molecular model (Ion Petre et. al). Transcription HSF+HSF<-> HSF 2 HSF+HSF 2 <->HSF 3 HSF 3 +HSE<->HSF 3 :HSE

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Heat shock response & Petri-net

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  1. Computational Biomodelling Lab. Department of Information Technologies,Åbo Akademi University, 20520 Turku, Finland Heat shock response & Petri-net

  2. The molecular model (Ion Petre et. al) • Transcription • HSF+HSF<->HSF2 • HSF+HSF2<->HSF3 • HSF3+HSE<->HSF3:HSE • HSF3:HSE->HSF3:HSE+HSP • Backregulation • HSP+HSF<->HSP:HSF • HSP+HSF2->HSP:HSF+HSF • HSP+HSF3->HSP:HSF+2HSF • HSP+HSF3:HSE->HSP:HSF+2HSF+HSE • Response to stress • PROT->MFP • HSP+MFP<->HSP:MFP • HSP:MFP->HSP+PROT • Protein degradation • HSP0

  3. o o o HSF HSF2 # of metabolites o o o o o o HSF:HSF2 Petri-net <=> Gene-net place transition Reactions tokens HSF+HSF2->HSF3

  4. k Types of reactions into Petri-net • 2HSF -> HSF2 • HSF3+HSE ->HSF3:HSE • HSP+HSF2->HSP:HSF+HSF • HSF3:HSE->HSF3:HSE+HSP • PROT->MFP (rewriting) • HSP0 (degradation) • HSF+HSF2<-> HSF3 (reverse) 2

  5. o o o o o o o o o transition transition Reaction HSF:HSF2 HSF+HSF2->HSF3 ->HSF+HSF2

  6. translation

  7. A Petri-net for the HSR model 37C 42C

  8. Incidence matrice 10x17

  9. Place invariant, Transition invariant P-invariant: x is a non-zero vector of size n (n=10) T-invariant: y is size of m (m=17)

  10. P-invariant *A P-invariant characterizes a token conservation rule for a set of places *An inv. x is minimal, if any inv. z: supp(z) is not subset of supp(x) - inv. 3 is minimal Deadlock…

  11. trivial T-invariant HS A T-invariant represents a multiset of transitions, which have altogether a zero effect on the marking

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