enabling grids for e-science infso-ri-031688 1 institute of mathematical problems of biology ras...
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INFSO-RI-031688 1
Enabling Grids for E-sciencE
Institute of mathematical problems of biology RAS
• Expertise in mathematical modeling and experimental data analysis in biology and medicine. Support and development of the Joint Centre for Computational Biology and Bioinformatics, http://www.jcbi.ru.
• EGEE-II major role:SA1 – organization and coordination of the EGEE-II Biology applications in Russia, involvement of new Russian RCs in Biomed VO. Porting in EGEE of new generation of biology applications – mathematical model of alive cell, www.mathcell.ru. RC support (IMPB RAS cluster). Support of basic Grid services. VO Biomed Support .
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Enabling Grids for E-sciencE
People• Administrative and scientific management:• Lakhno Victor
• Ustinin Mikhail
• Coordination:• Nazipova Nafisa
• Cluster support & training:• Zaitsev Aleksandr
• Applications & VO support• Fialko Nadezhda
• Filippov Sergey• Teplukhin Alexander• Tyulbasheva Gayane
Institute of mathematical problems of biology RAS
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Enabling Grids for E-sciencE
Institute of mathematical problems of biology RAS
The IMPB RAS RC (No. 106, ru-IMPB-LCG2, RU-PSN) presents
• 18 dual-processor Working Nodes of various productivity (Athlon 1200, 2000, P4 - 3000) with Gigabit Ethernet communication environment. Each of WNs is equipped by 1Gb RAM;
• CE is based on Core 2 Duo 2400 processor;• SE – on P4 – 3000 with ~0.9 Tb SATA RAID 5 disk
storage area.
The cluster is working under OS Scientific Linux 3.0.8. The middleware gLite 3.0 is installed.
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Enabling Grids for E-sciencE
Job maintenance system architecture
Institute of mathematical problems of biology RAS
•The special Job Maintenance System was developed which automatically allows Logging&Accounting, Job Submission, Job Status Monitoring, Job Queuing, Result Obtaining. Any registered user can use the program and the computational resources offered by EGEE infrastrucrure•.
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Enabling Grids for E-sciencE
MATHCELL LIBRARY MODELS
• software for modeling the electron transfer in DNA molecule;
• simulation model of electron transfer on inner photosynthetic membrane in chloroplasts;
• software for calculation of dissolution energy of biomolecules in water by Monte-Carlo method
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Enabling Grids for E-sciencE
Сharge transfer in DNA
In order to estimate the average value of macroscopic physical parameters one has to calculate the large number of realizations.
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Enabling Grids for E-sciencE
Simulation model of electron transfer on photosynthetic membrane
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Enabling Grids for E-sciencE
Calculation of dissolution energy of biomolecules in
water by Monte Carlo method
Input data:
• absolute temperature of water
• the molecule structure description in
the PDB-like format
Usage:• estimation of dissolution energy of molecules from homologous sequences,
• estimation of enthalpic or entropic effects of dissolution from temperature dependences
• compound identification by dissolution characteristics
• valuation of conformational characteristics of molecule in liquid environment
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Enabling Grids for E-sciencE
Future development of MathCell
In the near future IMPB RAS is planning to deploy in EGEE a software tool to calculate a charge transfer along electron transport chain in mitochondria of eukaryotic cells 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.