1 / 11

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

bconner
Télécharger la présentation

Heat shock response & Petri-net

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related