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.
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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