Computational Biomodelling Lab. Department of Information Technologies,

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Computational Biomodelling Lab. Department of
Information Technologies,Еbo Akademi University,
20520 Turku, Finland

• Heat shock response Petri-net

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The molecular model (Ion Petre et. al)

• Transcription
• HSFHSFlt-gtHSF2
• HSFHSF2lt-gtHSF3
• HSF3HSElt-gtHSF3HSE
• HSF3HSE-gtHSF3HSEHSP
• Backregulation
• HSPHSFlt-gtHSPHSF
• HSPHSF2-gtHSPHSFHSF
• HSPHSF3-gtHSPHSF2HSF
• HSPHSF3HSE-gtHSPHSF2HSFHSE

• Response to stress
• PROT-gtMFP
• HSPMFPlt-gtHSPMFP
• HSPMFP-gtHSPPROT
• Protein degradation
• HSP?0

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Petri-net ltgt Gene-net
place
transition
Reactions
tokens
HSFHSF2-gtHSF3
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Types of reactions into Petri-net

• 2HSF -gt HSF2
• HSF3HSE -gtHSF3HSE
• HSPHSF2-gtHSPHSFHSF
• HSF3HSE-gtHSF3HSEHSP
• PROT-gtMFP (rewriting)
• HSP?0 (degradation)
• HSFHSF2lt-gt HSF3 (reverse)

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5
transition
Reaction
HSFHSF2
HSFHSF2-gtHSF3
-gtHSFHSF2
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translation
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A Petri-net for the HSR model
37C
42C
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Incidence matrice 10x17
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Place invariant, Transition invariant
P-invariant x is a non-zero vector of size n
(n10)
T-invariant y is size of m (m17)
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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
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T-invariant
HS
A T-invariant represents a multiset of
transitions, which have altogether a zero effect
on the marking