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Reachability Analysis of Rule based Models

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83 pages
MPRI Reachability Analysis of Rule-based Models [ICCMSE'07,VMCAI'08] Jérôme Feret Laboratoire d'Informatique de l'École Normale Supérieure INRIA, ÉNS, CNRS feret January 2012

  • laboratoire d'informatique de l'ecole normale

  • local views

  • pathway

  • rule-based models

  • modeling signaling


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MPRI
Reachability Analysis
of Rule-based Models
[ICCMSE’07,VMCAI’08]
Jérôme Feret
Laboratoire d’Informatique de l’École Normale Supérieure
INRIA, ÉNS, CNRS

January 2012
ferethttp://www.di.ens.fr/Joint-work with...
Vincent DanosWalter Fontana
EdinburghHarvard Medical School
Russ Harmer Jean Krivine
Paris VII Paris VII
Jérôme Feret 2 January 2012Overview
1. Introduction
2. Kappa language
3. Local views
4. Local set of chemical species
5. Local rule systems
6. Decontextualization
7. Conclusion
Jérôme Feret 3 January 2012Modeling signaling pathway
Signaling pathway:
-- A cell measures (i.e. checks thresholds, integrates, compares) the
concentration of some proteins in order to make decisions.
-- Many proteins (enzymes, receptors, transport molecules) are in-
volved.
-- They interact by binding with each other and activating each other.
rule-based models:
-- A site graph-based rewrite language.
-- Description level matches with biologists’ observation and manipu-
lation level.
Static analysis:
We propose some static analysis tools in order to:
-- help the design of rule-based models;
-- compute (abstract) the properties of rule-based models.
Jérôme Feret 4 January 2012A single story
Jérôme Feret 5 January 2012A concurrent story
Jérôme Feret 6 January 2012Overshoot
When we combine the two stories. . .
. . . we get an overshoot.
Jérôme Feret 7 January 2012Overview
1. Introduction
2. Kappa language
3. Local views
4. Local set of chemical species
5. Local rule systems
6. Decontextualization
7. Conclusion
Jérôme Feret 8 January 2012A chemical species
r RR r
l
l
r
r
E E
E(r!1), R(l!1,r!2), R(r!2,l!3), E(r!3)
Jérôme Feret 9 January 2012A Unbinding/Binding Rule
R rR r
ll
rr
EE
E(r), R(l,r) ! E(r!1), R(l!1,r)
Jérôme Feret 10 January 2012