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Enabling Grids for E-sciencE Construction of a Mathematical Model of a Cell as a Challenge for Science in the 21 Century and EGEE Project Victor Lakhno Institute of Mathematical Problems of Biology RAS EGEE User Forum CERN, 01-03.03.2006

  1. Enabling Grids for E-sciencE Construction of a Mathematical Model of a Cell as a Challenge for Science in the 21 Century and EGEE Project Victor Lakhno Institute of Mathematical Problems of Biology RAS EGEE User Forum CERN, 01-03.03.2006 www.eu-egee.org INFSO-RI-508833

  2. www.mathcell.ru Enabling Grids for E-sciencE EGEE User Forum, CERN, 01-03.03.2006 2 INFSO-RI-508833

  3. About the project Enabling Grids for E-sciencE The project "MATHEMATICAL CELL" is directed on creation of the multipurpose environment for studies in biology of a living cell by integration of mathematical models, resources in bioinformatics, and computational facilities. It will help to produce a new knowledge about a living cell, as self-consistent dynamic system. The project is carried out by the Institute of Mathematical Problems of Biology in frames of the EGEE project. It leads to the gradual deployment of new applications in computational biology on EGEE infrastructure. EGEE User Forum, CERN, 01-03.03.2006 3 INFSO-RI-508833

  4. 3D model of the cell Enabling Grids for E-sciencE EGEE User Forum, CERN, 01-03.03.2006 4 INFSO-RI-508833

  5. Encyclopedia Enabling Grids for E-sciencE physical and mathematical knowledge ENCYCLOPAEDIA biological knowledge EGEE User Forum, CERN, 01-03.03.2006 5 INFSO-RI-508833

  6. Links Enabling Grids for E-sciencE EGEE User Forum, CERN, 01-03.03.2006 6 INFSO-RI-508833

  7. Library of mathematical models Enabling Grids for E-sciencE EGEE User Forum, CERN, 01-03.03.2006 7 INFSO-RI-508833

  8. С harge transfer in DNA Enabling Grids for E-sciencE In order to estimate the average value of macroscopic physical parameters one has to calculate the large number of realizations. EGEE User Forum, CERN, 01-03.03.2006 8 INFSO-RI-508833

  9. Simulation models Enabling Grids for E-sciencE Charge transfer in mytochondrion membrane Cytochrom C Protein complexes, built in a membrane Real mytochondrion membrane Ubiquinon Membrane EGEE User Forum, CERN, 01-03.03.2006 9 INFSO-RI-508833

  10. Cellular metabolism Enabling Grids for E-sciencE EGEE User Forum, CERN, 01-03.03.2006 10 INFSO-RI-508833

  11. Mathematical modeling of cell metabolism Enabling Grids for E-sciencE EGEE User Forum, CERN, 01-03.03.2006 11 INFSO-RI-508833

  12. Future development of MathCell Enabling Grids for E-sciencE In the near future IMPB RAS is planning to deploy in EGEE a software tool to calculate a charge transfer on inner membranes of some compartments of eukaryotic cells (mitochondria and chloroplasts) through direct simulation of charge transfer with regard to the detailed structure of biomembranes containing various molecular complexes. Next on the agenda is a software tool to calculate metabolic reaction pathways in compartments of a cell as well as the dynamics of gene networks. Further development of the MathCell project implies integration of individual components of the model into an integrated program system which would enable modeling of cell processes at all levels – from microscopic to macroscopic scales and from picoseconds to the scales comparable with the cell lifetime. Such modeling will naturally require combining of computational and commutation resources provided by EGEE project and their merging into an integrated computational medium. EGEE User Forum, CERN, 01-03.03.2006 12 INFSO-RI-508833

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