High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

Jaziri, Faouzi; Peyretaillade, Éric; Peyret, Pierre; Hill, David R.C.

doi:10.1002/cpe.3412

Cited by 2 publications

(1 citation statement)

References 31 publications

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“…Jaziri et al [13], in their article High Performance Computing of Oligopeptides Complete Backtranslation applied to DNA Microarray Probe Design, tackle the issue of large-scale backtranslation of oligopeptides, a step of generating all possible nucleic acid sequences from a protein sequence, which is needed for the discovery of new organisms. Because back translation is a time-consuming task that can generate very large quantities of data, authors propose an efficient distributed algorithm to compute a complete back translation of several hundreds of oligopeptides for functional Deoxyribose Nucleic Acid microarrays.…”

Section: Accelerators Multicore and Special-purpose Hybrid Architecmentioning

confidence: 99%

New advances in High Performance Computing and simulation: parallel and distributed systems, algorithms, and applications

Smari

Bakhouya

Fiore

et al. 2016

Concurrency and Computation

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INTRODUCTIONRecent developments in research and technological studies have shown that High Performance Computing (HPC) will indeed lead to advances in several areas of Science, engineering, and technology, permitting the successful completion of more computationally intensive and dataintensive problems such as those in healthcare, biomedical and biosciences, climate and environmental changes, multimedia processing, design and manufacturing of advanced materials, geology, astronomy, chemistry, physics, and even financial systems. However, further research is required for developing computing infrastructures, models to support newly evolving architectures, programming paradigms, tools to simulate and evaluate new approaches and solutions, and programming languages that are appropriate for the new and emerging domains and applications.The development of the HPC infrastructure has been accelerated by the advances in silicon technology, which permitted the design of complex systems able to incorporate many hardware and software blocks and cores. More precisely, recent rapid advances in technology and design tools enabled engineers to design systems with hundreds of cores, called multi-processor system-on-chip. These systems are composed of several processing elements, that is, dedicated hardware and software components that are interconnected by an on-chip interconnect. According to Moore's law, the number of cores on-chip will double every 18 months; therefore, thousands of cores-on-chip will be integrated in the next 20 years to meet the power and performance requirements of applications.Moreover, current trends on the road to exascale are moving toward the integration of more and more cores into a single chip [1,2]. For example, accelerators and heterogeneous processing offer some opportunities to greatly increase computational performance and to match increasing application requirements [3]. Engineering these computing systems is one of the most dynamic fields in modern Science and technology. That said, there will continue to be a growing demand for more powerful HPC in the upcoming years, not just to tackle basic mounting computing needs but also to lay out the foundations for the HPC market that is becoming potentially larger than the desktop/laptop computer market. Furthermore, HPC is turning out to be a major source of hope for future applications development that require greater amounts of computing resources in various modern Science domains such as bioengineering, nanotechnology, and energy where HPC capabilities are mandatory in order to run simulations and perform visualization tasks.At the time of writing this editorial, petaflop computing is well established [4]. Several architectures are making major breakthroughs: commodity, accelerators on commodity, and special-purpose cores. All of top 500 systems are based on multicore technologies [5]. HPC usage is growing considerably, especially in industry. And significant efforts toward establishing exascale are underway. At the same time, several challenge...

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Section: Accelerators Multicore and Special-purpose Hybrid Architecmentioning

confidence: 99%

New advances in High Performance Computing and simulation: parallel and distributed systems, algorithms, and applications

Smari

Bakhouya

Fiore

et al. 2016

Concurrency and Computation

View full text Add to dashboard Cite

show abstract

Granular Fuzzy Possibilistic C-Means Clustering approach to DNA microarray problem

Truong

Ngo

Pedrycz

2017

Knowledge-Based Systems

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High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

Cited by 2 publications

References 31 publications

New advances in High Performance Computing and simulation: parallel and distributed systems, algorithms, and applications

New advances in High Performance Computing and simulation: parallel and distributed systems, algorithms, and applications

Granular Fuzzy Possibilistic C-Means Clustering approach to DNA microarray problem

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