Internal coarse graining of molecular systems

Jérôme Feret

Description

CS2Bio Internal coarse-graining of molecular systems? [PNAS'09,LICS'10] Jérôme Feret Laboratoire d'Informatique de l'École Normale Supérieure INRIA, ÉNS, CNRS ? This research has been done during my Post-Doc at Harvard Medical School June 10, 2010

• laboratoire d'informatique de l'ecole normale


• msb4100014-e2 molecularsystemsbiology2005


• internal coarse-graining

Sujets

• Harmer
• Fontana
• Krivine

Informations

• Publié par: pefav
• Nombre de lectures: 22
• Langue: English
• Poids de l'ouvrage: 4 Mo

Extrait

CS2Bio

Internal coarse-graining of molecular systems ∗

[PNAS’09,LICS’10]

Jérôme Feret Laboratoire d’Informatique de l’École Normale Supérieure INRIA, ÉNS, CNRS

∗This research has been done during my Post-Doc at Harvard Medical School

June 10, 2010

Jérôme Feret

Joint-work with...

Walter Fontana Harvard Medical School

Russ Harmer Paris VII (Harvard Medical School)

2

Vincent Danos Edinburgh

Jean Krivine Paris VII

June 10, 2010

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Overview

Context and motivations

Handmade ODEs

Abstract interpretation framework

Kappa

Concrete semantics

Abstract semantics

Conclusion

Jérôme Feret

3

June 10, 2010

Jérôme

Feret

Signalling

4

Pathways

Eikuch,

June

2007

10, 2010

Jérôme Feret

Pathway

maps

Oda, Matsuoka, Funahashi, Kitano,

5

Molecular Systems

Biology, 2005

June 10, 2010

Differential models

 xd dt 1 = −k 1 ∙x 1 ∙x 2 +k −1 ∙x 3 d d x 2 = −k 1 ∙x 1 ∙x 2 +k −1 ∙x 3 t d d x t 3 =k 1 ∙x 1 ∙x 2 −k −1 ∙x 3 +2∙k 2 ∙x 3 ∙x 3 −k −2 ∙x 4 )   dt dx 4 =k 2 ∙x 2 k 2 ∙x 4 + p v 4 4 ∙ +x x 5 5 − (k 3 ∙x 4 −k −3 ∙x 5 ) − 3 dx 5 =∙ ∙ ∙ dt .   dx n = −k 1 ∙x 1 ∙c 2 +k −1 ∙x 3 dt

−do not describe the structure of molecules; −combinatorial explosion:forces choices that are not principled; −a nightmare to modify.

Jérôme Feret

6

June 10, 2010

A gap between two worlds

Two levels of description: 1. Databases of proteins interactions in natural language + documented and detailed description + transparent description −cannot be interpreted 2. ODE-based models + can be integrated −opaque modelling process, models can hardly be modified −there are also some scalability issues.

Jérôme Feret

7

June 10, 2010