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Information × Registration Number 0211U002894, 0110U004853 , R & D reports Title Development of new highly-parallel GRID computation methods for the systematic analysis of liver regeneration processes using gene regulatory network models based on microarray experiments data popup.stage_title Head Obolenskaya Maria Yurievna, Registration Date 09-03-2011 Organization Institute of Molecular Biology and Genetics of NASU popup.description2 We have prepared the theoretical basis for algorithms of development and reconstruction for modeling networks of gene regulation; it was chosen the platform for comparison of accuracy of methods for gene regulation networks modeling and their algorithmic implementations, namely as the platform we selected data from DREAM Challenge project, because along with "gold standard" there are also available ready software (Matlab scripts) to assess similarity of our results to the results of "standard"; we have analyzed 21 programs for the reconstruction of gene regulation networks and ARACNE program was selected because only it allows parallelization at the data level; performers of computing part of the project received personal certificates of UGRID Center, and recieved personal access (username / password) to the cluster of the Institute of Molecular Biology and Genetics and conducted primary grid computing; for parallel computing it has been written several scripts using Python language, which split the data and automatically generated xrsl-files; the main calculations were carried out on clusters nordu.hpcc.ntu-kpi.kiev.ua and cluster.immsp.kiev.ua; parallelized computing more than 6 times shortened the time needed for test problem solving with the data for 4000 genes of enteric bacteria. Obtained results had high degree of similarity to the results of "gold" standard. This work is planned to solve problems for 40 000 genes of higher organisms. We have shown the possibility to achieve high parallelism in reconstruction of gene regulation networks based on information theory: it was demonstrated a high degree of similarity between obtained results to the results of "gold" standard. Reconstruction of gene regulation networks of higher organisms, the goal of the project, as opposed to simpler organisms requires much more RAM and parallelization, which makes grid technology indispensable for solving such problems. Product Description popup.authors Куклін Андрій Володимирович Оболенська Марія Юріївна Синявський Олександр Леонідович Слончак Андрій Миколайович Токовенко Богдан Тарасович Фролова Аліна Олександрівна popup.nrat_date 2020-04-02 Close