The Silicon Cell:

Towards Computing the Living Cell

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Aim

The long-term goal of the Silicon Cell Initiative Amsterdam is the computation of Life at the cellular level on the basis of the complete genomic, transcriptomic, proteomic, metabolomic, and cell-physiomic information that will become available in the forthcoming years.

Research focus

• regulatory networks (metabolic, signal transduction, gene expression)
• structure and functional organization of cell nucleus
• dynamic architecture of cells

Model integration to calculate two real cells

• E. coli (prokaryote)
• S. cerevisiae (baker's yeast, eukaryote)

Projects

• Mathematics and Computation for the Systems Biology of Cells (NWO-CLS)
• Simulation of Developmental Regulatory Networks (NWO-CLS)
• Mesoscale Simulation Paradigms in the Silicon Cell (NWO-Wiskunde_Toegepast)

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Workshop Spatial fluctuations in cellbiology
CWI, Amsterdam, September 27-28, 2007

URL: http://www.cwi.nl/projects/sic/sym2007/

Aim: To bring together mathematicians, biophysicists, and biologists (experimentalists and theoreticians) to discuss various aspects of stochasticity in spatial phenomena that occur in cellular biology: "How should we measure such stochastic effects?", "What are proper mathematical descriptions for such processes?", "How to compute those models?", and "When can fluctuations become significant at the macroscopic level?". The emphasis will be on integration of theory with experiment and an overview of the present limitations in carrying out such studies.

Speakers: Dennis Bray (Cambridge), Arup Chakraborty (MIT), Johan Elf (Harvard), Dorus Gadella (SILS), Caroline Horton (SBC, Liverpool), and Jeroen van Zon (Imperial College)

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