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Second-generation sequencing (SGS) and Third-Generation Sequencing (TGS) are exponentially increasing the amount of data available for bioinformatics analyses. Severa! strategies have been devised to cope with such challenge. Firstly, microprocessors with severa! cores have been designed, for parallel processing. Secondly, new bioinformatics algorithms have been developed, to exploit such parallel-processing capabilities. Thirdly, heterogeneous architectures using both Central Processing Units (CPU) and Graphics Processing Units (GPU) can be further deployed, to speed-up bioinformatics algorithms. A Highly Heterogeneous Smith-Waterman (HHeterSW) algorithm is described, as a proof of concept for such latter strategy. This way, a 2.58-fold speed increase was obtained, when compared to non-hybrid implementations. Likewise, it was fas ter in 78% of tests, when compared to popular Basic Local-Alignment Search Too! (BLAST), effectively exploiting available hardware.

We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification/ traceability), inclu

Current trends in computer programming look for solutions in the challenging task of porting and optimizing existing algorithms to many-core architectures with tens of Central Processing Units (CPUs). Yet, the lack of standardized general-purpose parallel programming and porting methodologies represents the main bottleneck on these developments. We have focused on bioinformatics applied to genomics in general and the so-called >Next-Generation> Sequencing (NGS) in particular, in order to study the viability and cost of porting and optimizing well known algorithms to a many-core architecture. Three different methods are tackled in order to implement existing algorithms in Tile64, corresponding to a microprocessor containing 64 CPUs, each of them being capable of executing an independent Linux operating system. Three different approaches have been explored: (i) implementation of the Needleman-Wunsch/Smith-Waterman pairwise aligner from scratch; (ii) direct translation of the Message Passing Interface (MPI) C++ ABySS assembly algorithm with changes on the communication layer; and (iii) migration of the ClustalW tool, parallelizing only the most time-consuming stage. The performance-gain/development-cost tradeoffs indicate that the Tile64 microprocessor has the potential to increase the performance of bioinformatics in an unprecedented way for a standalone Personal Computer (PC). Yet, the effective exploitation of these parallel implementations requires a detailed understanding of the peculiar many-core characteristics when migrating previous non-parallel source codes. © 010 Elsevier B.V. All rights reserved.

ew analytical methodologies, like the so-called "next-generation sequencing" (NGS), allow the sequencing of full genomes with high speed and reduced price. Yet, such technologies generate huge amounts of data that demand large raw computational power. Many-core technologies can be exploited to overcome the involved bioinformatics bottleneck. Indeed, such hardware is currently in active development. We have developed parallel bioinformatics algorithms for many-core microprocessors containing 64 cores each. Thus, the MC64 web platform allows executing high-performance alignments (Needleman-Wunsch, Smith-Waterman and ClustalW) of long sequences. The MC64 platform can be accessed via web browsers, allowing easy resource integration into third-party tools. Furthermore, the results obtained from the MC64 include time-performance statistics that can be compared with other platforms.

Current computer engineering evolves at an accelerated pace, with hardware advancing towards new chip multiprocessors (CMP) architectures and with supporting software gearing towards new programming and abstraction paradigms, to obtain the maximum efficiency of the hardware at a low cost. In this context, Tilera Corporation has developed a brand new CMP architecture with 64 cores (tiles) called Tile64, and has launched several Peripheral Component Interconnect Express (PCIe) cards to be used and monitored from a host Personal Computer (PC). These cards may execute parallel applications built in C/C++ and compiled with the Tile-GCC compiler. We have previously demonstrated the usefulness of the Tile64 architecture for bioinformatics [S. Gálvez, D. Díaz, P. Hernández, F.J. Esteban, J.A. Caballero, G. Dorado, Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment, Bioinformatics, 26 (2010) 683-686]. We have chosen a bioinformatics algorithm to test this many-core Tile64 architecture because of actual bioinformatics challenging needs: data-intensive workloads, space and time-consuming requirements and massive calculation. This algorithm, known as Needleman-Wunsch/Smith-Waterman (NW/SW), obtains an optimal sequence alignment in quadratic time and space cost, yet requires to be optimized to take full advantage of computing parallelization. In this paper we redesign, implement and fine-tune this algorithm, introducing key optimizations and changes that take advantage of specific Tile64 characteristics: RISC architecture, local tile's cache, length of memory word, shared memory usage, RAM file system, tile's intercommunication and job selection from a pool. The resulting algorithm - named MC64-NW/SW for Multicore64 Needleman-Wunsch/Smith-Waterman - achieves a gain of ∼1000% when compared with the same algorithm on a ×86 multi-core architecture. As far as we know, our NW/SW implementation is the fastest ever pub

Motivation: Bioinformatics algorithms and computing power are the main bottlenecks for analyzing huge amount of data generated by the current technologies, such as the 'next-generation' sequencing methodologies. At the same time, most powerful microprocessors are based on many-core chips, yet most applications cannot exploit such power, requiring parallelized algorithms. As an example of next-generation bioinformatics, we have developed from scratch a new parallelization of the Needleman-Wunsch (NW) sequence alignment algorithm for the 64-core Tile64 microprocessor. The unprecedented performance it offers for a standalone personal computer (PC) is discussed, optimally aligning sequences up to 20 times faster than the non-parallelized version, thus saving valuable time. Availability: This algorithm is available as a free web service for the scientific community at http://www.sicuma.uma.es/multicore. The open source code is also available on such site. Contact: galvez@uma.es Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press.

Recoil nucleon transferred polarization observables in coincidence quasielastic electron scattering are studied within the relativistic distorted wave impulse approximation. Results for response functions and polarization asymmetries are discussed for proton knockout from p1/2, p 3/2, and s1/2 shells in 16O. The impact of spinor distortion is examined by comparing the fully relativistic calculation with results obtained by projecting out the negative-energy components. In particular, a careful analysis of effects linked to the description of the bound and scattered relativistic nucleon wave functions is presented. The high sensitivity of some polarization observables to the dynamical enhancement of the lower components, already shown within the relativistic plane wave impulse approximation, is proven to be maintained in the relativistic distorted wave approach. Semi-relativistic approaches based on the effective momentum approximation are also studied. Finally, comparison with experimental data and a brief analysis of effects linked to medium modified form factors is presented. ©2004 American Physical Society

An analysis of the effects of meson exchange and isobar currents in exclusive (e,e′p) processes from 16O under quasifree kinematics is presented. A model that has probed its feasibility for inclusive quasielastic (e,e′) processes is considered. Sensitivity to final state interactions between the outgoing proton and the residual nucleus is discussed by comparing the results obtained with phenomenological optical potentials and a continuum nuclear shell-model calculation. The contribution of the meson exchange and isobar currents to the response functions is evaluated and compared to previous calculations, which differ notably from our results. These two-body contributions cannot solve the puzzle of the simultaneous description of the different responses experimentally separated. ©1999 American Physical Society

The recent Pb-208(e,e'p)Tl-207 data from NIKHEF-K at high missing momentum (p(m)>300 MeV/c) are compared to theoretical results obtained with a fully relativistic formalism previously applied to analyze data on the low missing momentum (p(m)<300 MeV/c) region. The same relativistic optical potential and mean-field wave functions are used in the two p(m) regions. The spectroscopic factors of the various shells are extracted from the analysis of the low-p(m) data and then used in the high-p(m) region. In contrast to previous analyses using a nonrelativistic mean-field formalism, we do not find a substantial deviation from the mean-field predictions other than that of the spectroscopic factors, which appear to be consistent with both low- and high-p(m) data. We find that the difference between results of relativistic and nonrelativistic formalisms is enhanced in the p(m)<0 region that will be interesting to explore experimentally.

We present results for response functions and asymmetries in the nuclear reactions Ar-37(e,e'n)Ar-36 and K-37(e,e'p) Ar-36 at quasifree kinematics. We compare PWIA results obtained using deformed HF wave functions with PWIA and DWIA results obtained assuming a spherical mean field. We show that the complex structure of the deformed orbitals can be probed by coincidence measurements with polarized beam and targets.

We study the properties of the spin-dependent one-body density in momentum space for odd-A polarized deformed nuclei within the mean field approximation. We derive analytic expressions connecting intrinsic and laboratory momentum distributions. The latter are related to observable transition densities in p-space that can be proved in one nucleon knockout reactions From polarized targets. It is shown that most of the information contained in the intrinsic spin-dependent momentum distribution is lost when the nucleus is not polarized. Results are presented and discussed for two prolate nuclei, Ne-21 and Mg-25, and for one oblate nucleus, Ar-37. The effects of deformation are highlighted by comparison to the case of odd-A nuclei in the spherical model.

We investigate the role of relativistic and nonrelativistic optical potentials used in the analysis of (e,e'p) data. We find that the relativistic calculations produce smaller (e,e'p) cross sections even in the case in which both relativistic and nonrelativistic optical potentials fit equally well the elastic proton-nucleus scattering data. Compared to the nonrelativistic impulse approximation, this effect is due to a depletion in the nuclear interior of the relativistic nucleon current, which should be taken into account in the nonrelativistic treatment by a proper redefinition of the effective current operator.

We present results for spectroscopic factors of the outermost shells in Ca-40 and Pb-208, which have been derived from the comparison between the available quasielastic (e, e'p) data from NIKHEF-K and the corresponding calculated cross sections obtained within a fully relativistic formalism. We include exactly the effect of Coulomb distortion on the electron wave functions and discuss its role in the extraction of the spectroscopic factors from experiment. Without any adjustable parameter, we find spectroscopic factors of about 70%, consistent with theoretical predictions. We compare our results with previous relativistic and nonrelativistic analyses of (e, e'p) data. In addition to Coulomb distortion effects, we discuss different choices of the nucleon current operator and also analyze the effects due to the relativistic treatment of the outgoing-distorted and bound nucleon wave functions.

https://patrimoniodigital.ucm.es/r/thumbnail/655738, https://patrimoniodigital.ucm.es/r/item/5322446645

Diálogo en el qual se resuelven varias dudas concernientes á la misma materia y algunas otras, p. 64-176, Diálogo en el qual se resuelven varias dudas concernientes á la misma materia y algunas otras, p. 64-176, Aguilar Piñal.Bib.S.XVIII, Sign.; ¶-4¶⁸, 5¶⁸⁻¹, A-L⁸

Ubicación del derecho de la protección del consumidor en Colombia; reseña histórica del origen y desarrollo del derecho de la protección del consumidor en Estados Unidos, Inglaterra, Europa y Colombia; y análisis de procedencia de la relación de consumo frente a los productos impresos en 3D.