Whole cell simulation a novel approach

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Whole cell simulation a novel approach

• Yves Sucaet
• BCB - Bioinformatics Computational Biology

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A grand challenge
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Systems biology

• Integrating the omics
• Holistic approach toward biological systems
• Big demand
• Pharmaceuticals / biotech
• Predict drug responses
• Agriculture
• Plant trials
• Start-up companies
• Gene Network Systems
• Entelos

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When will we be ready?
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Cell simulation environments

• E-Cell
• Jarnac / Jdesigner
• Industry
• Colon cancer cell
• 6,000 genes
• 450 parameters (pH, temperature...)

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Systems Biology Workbench
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A novel approach

• Stochastics
• Molecules don't know they're describing a random
  walk, or that they're answering to kinetic laws
• Provide a virtual 3D-environment
• Put molecules in
• Define reactions
• Let them roam free...
• Observe results

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Preliminary work

• Glycolysis pathway

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Glycolysis concentration variations
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Reaction efficiencies
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Cofactors
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Pyruvate inhibitor of hexokinase
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Additional features

• Change concentrations of species
• Switch reactions on/off in real-time
• Implement a gene transcription module
• Allow diffusion outside/inside the matrix
• Implement polymerization
• Glycogen-metabolism
• Translation

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Delegating complexity
Electron transport
Na/K pump
Photosynthesis
Transcription Translation
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Networking
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Chaining reactors

• Once diffusion is allowed, molecule species can
  diffuse from one matrix into another
• Different matrices can have different reactions
  and enzymes
• Compartmentalization
• Mitochondrion, chloroplast, nucleus, cell
  membrane
• Mimic spatial features by altering surface/volume
• Horizontal scalability of simulation
• Parallelization

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A single cell?
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Future plans
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Demo