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Congestion Game Scheduling Implementation for High-Throughput Virtual Drug Screening Using BOINC-Based Desktop Grid

  • Natalia Nikitina
  • Evgeny Ivashko
  • Andrei Tchernykh
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10421)

Abstract

Virtual drug screening is one of the most common applications of high-throughput computing. As virtual screening is time consuming, a problem of obtaining a diverse set of hits in a short time is very important. We propose a mathematical model based on game theory. Task scheduling for virtual drug screening in high-performance computational systems is considered as a congestion game between computing nodes to find the equilibrium solutions for best balancing between the number of interim hits and their chemical diversity. We present the developed scheduling algorithm implementation for Desktop Grid and Enterprise Desktop Grid, and perform comprehensive computational experiments to evaluate its performance. We compare the algorithm with two known heuristics used in practice and observe that game-based scheduling outperforms them by the hits discovery rate and chemical diversity at earlier steps.

Keywords

Drug discovery Virtual drug screening High-performance computing High-throughput computing Desktop grid BOINC Scheduling Game theory Congestion game 

Notes

Acknowledgments

This work is partially supported by the Russian Fund for Basic Research under grants no. 16-07-00622 and 15-29-07974, and CONACYT (Consejo Nacional de Ciencia y Tecnología, México) under grant no. 178415.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Natalia Nikitina
    • 1
  • Evgeny Ivashko
    • 1
  • Andrei Tchernykh
    • 2
  1. 1.Institute of Applied Mathematical ResearchKarelian Research Center, Russian Academy of SciencesPetrozavodskRussia
  2. 2.Computer Science DepartmentCICESE Research CenterEnsenadaMexico

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