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3 Computational Methods in Science and Technology

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Preprocessing and Storing High - Throughput Sequencing Data

Świercz A., Bosak B., Chłopkowski M., Hoffa A., Kasprzak M., Kurowski M., Piontek T., Błażewicz J.

Computational Methods in Science and Technology

2014

Vol. 20, No. 1

9--20

DNA sequencing is a process of recognizing DNA sequences of genomes. The process consists in reading short sequences, that are subsequences of a genome, and merging them into longer sequences, preferably the whole genome. In the first phase even billions of short sequences are read at once. To simplify and speed up the second phase, we develop a pipeline of preprocessing the initial set of short sequences that is removing low quality reads and duplicated reads.We also propose a method for preliminary joining overlapping sequences, which resulted in decreasing the cardinality of initial sets to 13.9% and 27.8%. We also examine possible ways to store the huge amount of experimental data. We compare different compression methods, from which the best appeared to be DSRC, developed for special type of text files containing short sequences and their quality. We test the parameters for TCP data transferring to find the best transfer rate.

Parallel Large Scale Simulations in the PL-Grid Environment

Kurowski K., Piontek T., Kopta P., Mamoński M., Bosak B.

Computational Methods in Science and Technology

2010

Vol. spec. iss. (1)

47-56

The growing demand for computational power causes that Grids are becoming mission-critical components in research and industry, offering sophisticated solutions in leveraging large-scale computing and storage resources. The nature a Grid in which resources are usually shared among multiple organizations offering resources under their control based on the “best effort” approach with no guarantee concerning the quality-of-service may be inadequate to support large-scale simulations. Requirements of such simulations often exceed capabilities of a single computing center causing the need to simultaneously allocate and synchronize resources belonging to many administrative domains whose functionality is missing in leading grid middlewares preventing researchers from executing large-scale simulations in grids. The paper presents tools and services that were designed to build multilayered infrastructure capable of dealing with computationally intensive large-scale simulations in the grid environment. The developed and deployed middleware enables computing clusters in different administrative domains to be virtually welded into a single powerful compute resource that can be treated as a quasi-opportunistic supercomputer. We describe the middleware developed in the QosCosGrid project and being enhanced under the PL-Grid national grid initiative, which provides advance reservation and resource co-allocation functionality as well as support for parallel large-scale applications based on OpenMPI (for C/C++ and Fortran) or ProActive for Java.

Programming Grid Applications with Gridge

Pukacki J., Kosiedowski M., Mikołajczak R., Adamski M., Grabowski P., Jankowski M., Kupczyk M., Mazurek C., Meyer N., Nabrzyski J., Piontek T., Russell M., Stroiński M., Wolski M.

Computational Methods in Science and Technology

2006

Vol. 12, nr 1

47-68

Not many fully integrated Grid solutions exist on today’s market. In this paper we present the PSNC’s Grid toolkit, called Gridge, which is fully integrated Grid environment, consisting of tools and Grid services to enable challenging scientific and commercial applications on the Grid.