Master Parisien de Recherche en Informatique
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Master Parisien de Recherche en Informatique Static Analysis of Kappa Models VMCAI 2008 Jérôme Feret Harvard Medical School École Normale Supérieure feret Joint work with Vincent Danos, Walter Fontana, and Jean Krivine December, 2007
- local views
- no cost
- ecole normale
- models automatically
- kappa models
- master parisien de recherche en informatique
Master Parisien de Recherche en Informatique
Static Analysis of Kappa Models
VMCAI 2008
Jérôme Feret
Harvard Medical School
École Normale Supérieure
Joint work with
Vincent Danos, Walter Fontana, and Jean Krivine
December, 2007
http://www.di.ens.fr/feretThe Team
Walter Fontana Vincent Danos
Harvard Medical School Paris VII
Jean Krivine Jérôme Feret
École polytechnique École normale supérieure
Jérôme Feret, LIENS 2 December, 2007Overview
1. Introduction
2. Kappa language
3. Local views
4. Local set of complexes
5. Local rule systems
6. Decontextualization
7. Conclusion
Jérôme Feret, LIENS 3 December, 2007Modeling signaling pathway
A cell measures (i.e. checks thresholds, integrates, compares) the con-
centration of some proteins in order to make decisions.
Many proteins (enzymes, receptors, transport molecules) are involved.
They interact by binding with each other and activating each other.
We want to track the evolution of some species:
There is a combinatorial blow-up.
Jérôme Feret, LIENS 4 December, 2007Why using modelling tools ?
Use a concise high-level description of what happens;
Share parts of models;
Derive quantitative models automatically:
-- run benchs of simulations,
-- modify initial conditions,
-- update/modify the model at no cost;
Use static analysis tools in order to check the consistency of a model:
-- dead rules detection,
-- control detection (which site controls which binding),
-- wrong species detection.
Jérôme Feret, LIENS 5 December, 2007Overview
1. Introduction
2. Kappa language
3. Local views
4. Local set of complexes
5. Local rule systems
6. Decontextualization
7. Conclusion
Jérôme Feret, LIENS 6 December, 2007A complex
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, LIENS 7 December, 2007A Unbinding/Binding Rule
R rR r
ll
rr
EE
E(r), R(l,r) ! E(r!1), R(l!1,r)
Jérôme Feret, LIENS 8 December, 2007Internal state
R Y1 R Y1
u p
l l
r r
E E
R(Y1u,l!1), E(r!1) ! R(Y1p,l!1), E(r!1)
Jérôme Feret, LIENS 9 December, 2007Don’t care, Don’t write
R Y1 R Y1
u p
r r
=
R Y1 R Y1
.u p
Jérôme Feret, LIENS 10 December, 2007
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