A very short platform tour

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A very short platform tour

• Ecole de Printemps dépigénomique
• Bordeaux 2006
• Charles Lales
• lales_at_labri.fr

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Minimal programming platform
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Advanced programming platform
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A clustering of platform
Generic platform of simulation
Specific platform of simulation
Specific simulator
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Generic platform NetLogo
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Generic platform NetLogo
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Generic platform StarLogo TNG
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Generic platform SeSam
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Generic platform Breve
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Specific platform SimBioDyn (100nm- 100µm)
1- Entities design
2- Interactions design
3- Simulation
4- Results analysis
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Specific platform SimBioDyn (100nm- 100µm)

• Author Pascal Ballet (demo avaible here!)

deformation of the membrane
enzymatic reaction
metastases
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Specific platform SimBioDyn (100nm- 100µm)
deformation of the membrane
enzymatic reaction
metastases
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Specific platform HSIM

• Aims to study the assembly, the movements and
  the dissociation of large numbers of molecules in
  a virtual cell.
• 3 steps
• Declaration of the molecules
• Reaction laws
• Initialisation
• Author Patrick Amar (demo avaible here!)

init (10000,AG)
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Specific platform HSIM
oblong membrane (after 15 min simulated time)
spherical membrane
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Specific code 3DSpi

• Aims to explore the minimal set of rules needed
  to generate large multi-protein structures.
• Results system behavior is very robust, in terms
  of the number and size of the structures
  generated.
• Author Guillaume Beslon

screen shot of the final state
after treatment
real life picture of speckles
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Specific code 3DSpi
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Specific code MitoMAS_membrane

• Aims to simulate the mitochondrial metabolism.
• Agent model
• Micellae