Internal coarse graining of molecular systems

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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


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CS2Bio
Internal coarse-graining of molecular systems
[PNAS09,LICS10]
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
1.
2.
3.
4.
5.
6.
7.
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
xddt1= −k1x1x2+k1x3 ddx2= −k1x1x2+k1x3 t ddxt3=k1x1x2k1x3+2k2x3x3k2x4) dtdx4=k2x2k2x4+pv44+xx55− (k3x4k3x5) 3 dx5 =∙ ∙ ∙ dt . dxn= −k1x1c2+k1x3 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
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