TOOLS FOR BIOMEDICAL DATA ARCHIVING IN UKRAINIAN GRID INFRASTRUCTURE

Authors

  • Oleksandr Sudakov
  • Andrii Salnikov
  • Ievgen Sliusar
  • Oleksandr Boretskyi

DOI:

https://doi.org/10.47839/ijc.12.4.610

Keywords:

Grid, Replication, Web service, Client, Storage, Protocol, Graphics, Anonymization, Image, DICOM.

Abstract

Tools for archiving and extraction of data in Ukrainian National Grid for end-users’ applications are proposed, implemented and deployed for practical applications in medical imaging, non-linear dynamics, and molecular biology. Proposed tools provide the facilities to utilize large distributed storage space in grid infrastructures for different practical tasks including desktop applications. Tools may be successfully used even when on client platforms it is impossible to setup grid middleware, use web browser interfaces or grid security infrastructure authentication. Tools consist of extensible client compatible with different software and hardware platforms; web service for data transfer; web service for transparent data replication on grid storage elements.

References

I. Foster and C.Kesselman, The Grid: Blueprint for a New Computing Infrastructure, Morgan Kaufmann, 1999.

M. Zynovyev, S. Svistunov, Y. Boyko, and O. Sudakov, Ukrainian grid infrastructure: Practical experience, Proceedings of the 4th IEEE Workshop on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications IDAACS’2007, September 6-8, 2007, Dortmund, Germany, pp. 165–169.

A. O. Salnikov, I. A. Sliusar, O. O. Sudakov, O. V. Savytskyi, A. I. Kornelyuk, MolDynGrid virtual laboratory as a part of Ukrainian Academic Grid infrastructure, Proceedings of the 5th IEEE International Workshop on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications IDAACS’2009, Rende (Cosenza), Italy, September 21-23, 2009, pp. 237-240.

A. Salnikov, R. Levchenko, O. Sudakov, Integrated grid environment for massive distributed computing in neuroscience, Proceedings of the 6th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications IDAACS’2011, Prague, Czech Republic, September 15-17, 2011, pp. 198-202.

O. E. Omel'chenko, M. Wolfrum, S. Yanchuk, Y. L. Maistrenko, O. Sudakov, Stationary patterns of coherence and incoherence in two-dimensional arrays of non-locally-coupled phase oscillators, Physical Review E, Vol. 85, Issue 3, 2012, Paper ID 036210.

O. Sudakov, M. Kononov, Ie. Sliusar, A. Salnikov, User clients for working with medical images in Ukrainian grid infrastructure, Proceedings of the 7th International IEEE Conference on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications IDAACS’2013, Berlin September 12-14, 2013, pр. 705-710.

Virtual organization membership service of Ukrainian national grid (UNG), National Taras Shevchenko University of Kyiv, 2011. [Online]. Available: http://grid.org.ua/voms/

Medical Grid-system for population research in the field of cardiology with electrocardiogram database 2012. [Online]. Available http://medgrid.immsp.kiev.ua/

Peter Mildenberger, Marco Eichelberg, and Eric Martin, Introduction to the DICOM standard, European Radiology, Vol. 12, Issue 4, 2002, pp. 920-927.

Johan Montagnat, Akos Frohner, Daniel Jouvenot, Christophe Pera, Peter Kunszt, Birger Koblitz, Nuno Santos, Charles Loomis, Romain Texier, Diane Lingrand, Patrick Guio, Ricardo Brito Da Rocha, Antonio Sobreira de Almeida, Zoltan Farkas, A secure grid medical data manager interfaced to the gLite middleware, Journal of Grid Computing (JGC), Vol. 6, Issue 1, Kluwer, March 2008, pp. 45–59, [Online]. Available http://modalis.i3s.unice.fr/softwares/mdm/

A. Shoshani, A. Sim, J. Gu, Storage resource managers: essential components for the grid, Grid Resource Management: State of the Art and Future Trends. Ed. by Jan Weglarz, Jarek Nabrzyski, Jennifer M. Schopf, Boston: Kluwer Academic Publishers, 2003, Vol. 64 of International Series in Operations Research & Management Science, pp. 329–348, ISBN: 978-1402075759.

I. Sliusar, M. Volzheva, Using grid infrastructure as a distributed fault-tolerant data storage for web services, Proceedings of the Second International Conference on Cluster Computing CC’2013, Ukraine, Lviv, June 3-5, 2013, pp. 266–268.

R. T. Fielding, R. N. Taylor, Principled design of the modern Web architecture, ACM Transactions on Internet Technology, Vol. 2, Issue 2, May 2002, pp. 115–150.

L. Dusseault, HTTP extensions for Web distributed authoring and versioning (WebDAV), Request for Comments: 4918. [Online]. Available http://tools.ietf.org/html/rfc4918

I. A. Sliusar, Automatic replication service for maintaining high availability of data in the grid-infrastructure, Control Systems and Machines, No. 4, 2012, pp. 63-69. (in Ukrainian)

B. Koblitz, N. Santos, V. Pose, The AMGA metadata service, Journal of Grid Computing, Springer Netherlands, Vol. 6, No. 1, 2008, pp. 61–76.

Libcurl: the multiprotocol file transfer library, 2013 [Online]. Available http://curl.haxx.se/

DCMTK: DICOM Toolkit, 2013 [Online]. Available http://dicom.offis.de/

T. Romanenko, V. Vishnevskiy, A. Boretskiy, Features of launching grid task with low computing time and big data transfers in a distributed repositories of "Medgrid" VO, Proceedings of the International Conference on Parallel and Distributed Computing Systems PDCS’2013, Ukraine, Kharkiv, March 13-14, 2013, pp. 266–268.

M. V. Kononov, O. A. Nagulyak, A. V. Netreba and A. A. Sudakov, Reconstruction in NMR by the method of signal matrix pseudoinversion, Radioelectronics and Communications Systems, Vol. 51, Num. 10, October 2008, pp. 531–533.

M. K. Novoselets, S. P. Radchenko, V. A. Tsubin, O. M. Gridko, Ultrasound introscopic image quantitative characteristics for medical diagnostics and refinements of physical noise rise reasons, Proceedings of the Medical Imaging, 1994, SPIE, Physics of Medical Imaging, Vol. 2163, 1994, pp. 442–446.

Downloads

Published

2014-08-01

How to Cite

Sudakov, O., Salnikov, A., Sliusar, I., & Boretskyi, O. (2014). TOOLS FOR BIOMEDICAL DATA ARCHIVING IN UKRAINIAN GRID INFRASTRUCTURE. International Journal of Computing, 12(4), 308-315. https://doi.org/10.47839/ijc.12.4.610

Issue

Section

Articles