computational biomodelling lab. department of information technologies, Åbo akademi university,...
Post on 21-Dec-2015
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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
1. HSF+HSF<->HSF2
2. HSF+HSF2<->HSF3
3. HSF3+HSE<->HSF3:HSE
4. HSF3:HSE->HSF3:HSE+HSP
Backregulation
5. HSP+HSF<->HSP:HSF6. HSP+HSF2->HSP:HSF+HSF
7. HSP+HSF3->HSP:HSF+2HSF
8. HSP+HSF3:HSE->HSP:HSF+2HSF+HSE
Response to stress
9. PROT->MFP10.HSP+MFP<->HSP:MFP11.HSP:MFP->HSP+PROT
Protein degradation
12.HSP0
3
Petri-net <=> Gene-net
place transition
Reactions
tokens
metabolites
HSF
HSF2 HSF:HSF2
HSF+HSF2->HSF3
# of
o o o
o o
o
o
o o
4
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)
• HSP0 (degradation)
• HSF+HSF2<-> HSF3 (reverse)
2
k
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…