Sergio Gálvez

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.

Parallelizing and optimizing a bioinformatics pairwise sequence alignment algorithm for many-core architecture

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. Galvez, D. Diaz, P. Hernandez, 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 tiles cache, length of memory word, shared memory usage, RAM file system, tiles 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 x86 multi-core architecture. As far as we know, our NW/SW implementation is the fastest ever published for a standalone PC when aligning a pair of sequences larger than 20kb.

MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures.

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), including the protected designation of origin, among other applications.

Intuitive Bioinformatics for Genomics Applications: Omega-Brigid Workflow Framework

The recent developments in life sciences and technology have produced large amounts of data in an extremely fast and cost-efficient way which require the development of new algorithms, coupled with massively parallel computing. Besides, biologists are usually non-programmers, thus demanding intuitive computer applications that are easy to use by means of a friendly GUI. In addition, different algorithms, databases and other tools usually lie on incompatible file formats, applications, operating systems and hardware platforms. It is therefore of paramount importance to overcome such limitations, so that bioinformatics becomes much more widely used amongst biologists. The main goal of our research project is to unify many of these existing bioinformatics applications and resources (local and remote) in one easy-to-use environment, independent of the computing platform, being a concentrator resource tool with a friendly interface. To achieve this, we propose a tool based on a new, open, free and well-documented architecture called Biomniverso. Two main elements make up such a tool: its kernel (Omega), which supplies services specifically adapted to allow the addition of new bioinformatics functionalities by means of plugins (like Minerva, which makes easy to detect SNP amongst a set of genomic data to discover fraudulent olive oil), and the interface (Brigid), which allows even non-programmer laboratory scientists to chain different processes into workflows and customize them without code writing.

Workflow Management Applied to Information Systems in Tourism

Nowadays, Workflow Management offers many advantages to the tourism industry due to the high degree of competition existing in this field and the need to quickly develop new products, offers, and services. This need for flexibility cannot be achieved without improving the processes involved in the information systems. Workflow technology facilitates this constant evolution, providing modeling methodologies and software to support all the processes taking place in a given company. This article studies the application of such technologies to businesses belonging to the tourism sector and focuses on the improvement of information systems to obtain higher customer satisfaction. To achieve this objective, a modeling methodology oriented toward customer satisfaction is presented. This is applied to the set of information systems involved in making a trip by plane and more specifically to aspects such as booking from intermediary companies and the information systems used by airline companies in airports.

Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW)

The Smith-Waterman algorithm has a great sensitivity when used for biological sequence-database searches, but at the expense of high computing-power requirements. To overcome this problem, there are implementations in literature that exploit the different hardware-architectures available in a standard PC, such as GPU, CPU, and coprocessors. We introduce an application that splits the original database-search problem into smaller parts, resolves each of them by executing the most efficient implementations of the Smith-Waterman algorithms in different hardware architectures, and finally unifies the generated results. Using non-overlapping hardware allows simultaneous execution, and up to 2.58-fold performance gain, when compared with any other algorithm to search sequence databases. Even the performance of the popular BLAST heuristic is exceeded in 78% of the tests. The application has been tested with standard hardware: Intel i7-4820K CPU, Intel Xeon Phi 31S1P coprocessors, and nVidia GeForce GTX 960 graphics cards. An important increase in performance has been obtained in a wide range of situations, effectively exploiting the available hardware.

MC64-Cluster: A Many-Core CPU Cluster for Bioinformatics Applications

The current developments in life sciences face a big challenge, with the need of dealing with huge amounts of data and the increasing demand of computational resources, both in hardware and in software, pushing the limits of the available state-of-the-art at an affordable price. This paper introduces a computer cluster whose building blocks are the first commercially available many-core CPU systems: the Tile64 by Tilera Corporation, packed in PCIe cards (TILExpress-20G). We have developed the main software components of the cluster (resource manager and scheduler) and a communication library, in order to offer a high-performance general-purpose platform to speedup bioinformatics applications.

Many-Core Processor Bioinformatics and Next-Generation Sequencing

The new massive DNA sequencing methods demand both computer hardware and bioinformatics software capable of handling huge amounts of data. This paper shows how the many-core processors (in which each core can execute a whole operating system) can be exploited to address problems which previously required expensive supercomputers. Thus, the Needleman-Wunsch/Smith-Waterman pairwise alignments will be described using long DNA sequences (>100 kb), including the implications for progressive multiple alignments. Likewise, assembling algorithms used to generate contigs on sequencing projects (therefore, using short sequences) and the future in peptide (protein) folding computing methods will be also described. Our study also integrates the last trends in many-core processors and their applications in the field of bioinformatics.

MC64: A Web Platform to Test Bioinformatics Algorithms in a Many-Core Architecture

New 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.

Electronic Invoicing for a Hotel Management Computer Network System

The current work is part of a larger research and development project undertaken by the Department of Computer Languages and Science at the University School of Tourism in Malaga University, in collaboration with certain software development companies plus the support of more than fifteen hotels in Malaga and Almeria, Spain.