Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, and Evaluations

Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences\u27 structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes. In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method encapsulates stereo-chemical properties of sequence residues and their substitution probabilities into a tree-structure scoring scheme. This new technique provides a reliable scoring scheme with low computational complexity. In addition to the new scoring scheme, we have designed an overlapping sequence clustering algorithm to use in our new three multiple sequence alignment algorithms. One of our alignment algorithms uses a dynamic weighted guidance tree to perform multiple sequence alignment in progressive fashion. The use of dynamic weighted tree allows errors in the early alignment stages to be corrected in the subsequence stages. Other two algorithms utilize sequence knowledge-bases and sequence consistency to produce biological meaningful sequence alignments. To improve the speed of the multiple sequence alignment, we have developed a parallel algorithm that can be deployed on reconfigurable computer models. Analytically, our parallel algorithm is the fastest progressive multiple sequence alignment algorithm

Parallel PAB3D: Experiences with a Prototype in MPI

PAB3D is a three-dimensional Navier Stokes solver that has gained acceptance in the research and industrial communities. It takes as computational domain, a set disjoint blocks covering the physical domain. This is the first report on the implementation of PAB3D using the Message Passing Interface (MPI), a standard for parallel processing. We discuss briefly the characteristics of tile code and define a prototype for testing. The principal data structure used for communication is derived from preprocessing "patching". We describe a simple interface (COMMSYS) for MPI communication, and some general techniques likely to be encountered when working on problems of this nature. Last, we identify levels of improvement from the current version and outline future work

A decentralized framework for cross administrative domain data sharing

Federation of messaging and storage platforms located in remote datacenters is an essential functionality to share data among geographically distributed platforms. When systems are administered by the same owner data replication reduces data access latency bringing data closer to applications and enables fault tolerance to face disaster recovery of an entire location. When storage platforms are administered by different owners data replication across different administrative domains is essential for enterprise application data integration. Contents and services managed by different software platforms need to be integrated to provide richer contents and services. Clients may need to share subsets of data in order to enable collaborative analysis and service integration. Platforms usually include proprietary federation functionalities and specific APIs to let external software and platforms access their internal data. These different techniques may not be applicable to all environments and networks due to security and technological restrictions. Moreover the federation of dispersed nodes under a decentralized administration scheme is still a research issue. This thesis is a contribution along this research direction as it introduces and describes a framework, called \u201cWideGroups\u201d, directed towards the creation and the management of an automatic federation and integration of widely dispersed platform nodes. It is based on groups to exchange messages among distributed applications located in different remote datacenters. Groups are created and managed using client side programmatic configuration without touching servers. WideGroups enables the extension of the software platform services to nodes belonging to different administrative domains in a wide area network environment. It lets different nodes form ad-hoc overlay networks on-the-fly depending on message destinations located in distinct administrative domains. It supports multiple dynamic overlay networks based on message groups, dynamic discovery of nodes and automatic setup of overlay networks among nodes with no server-side configuration. I designed and implemented platform connectors to integrate the framework as the federation module of Message Oriented Middleware and Key Value Store platforms, which are among the most widespread paradigms supporting data sharing in distributed systems

New advances in vehicular technology and automotive engineering

An automobile was seen as a simple accessory of luxury in the early years of the past century. Therefore, it was an expensive asset which none of the common citizen could afford. It was necessary to pass a long period and waiting for Henry Ford to establish the first plants with the series fabrication. This new industrial paradigm makes easy to the common American to acquire an automobile, either for running away or for working purposes. Since that date, the automotive research grown exponentially to the levels observed in the actuality. Now, the automobiles are indispensable goods; saying with other words, the automobile is a first necessity article in a wide number of aspects of living: for workers to allow them to move from their homes into their workplaces, for transportation of students, for allowing the domestic women in their home tasks, for ambulances to carry people with decease to the hospitals, for transportation of materials, and so on, the list don’t ends. The new goal pursued by the automotive industry is to provide electric vehicles at low cost and with high reliability. This commitment is justified by the oil’s peak extraction on 50s of this century and also by the necessity to reduce the emissions of CO2 to the atmosphere, as well as to reduce the needs of this even more valuable natural resource. In order to achieve this task and to improve the regular cars based on oil, the automotive industry is even more concerned on doing applied research on technology and on fundamental research of new materials. The most important idea to retain from the previous introduction is to clarify the minds of the potential readers for the direct and indirect penetration of the vehicles and the vehicular industry in the today’s life. In this sequence of ideas, this book tries not only to fill a gap by presenting fresh subjects related to the vehicular technology and to the automotive engineering but to provide guidelines for future research. This book account with valuable contributions from worldwide experts of automotive’s field. The amount and type of contributions were judiciously selected to cover a broad range of research. The reader can found the most recent and cutting-edge sources of information divided in four major groups: electronics (power, communications, optics, batteries, alternators and sensors), mechanics (suspension control, torque converters, deformation analysis, structural monitoring), materials (nanotechnology, nanocomposites, lubrificants, biodegradable, composites, structural monitoring) and manufacturing (supply chains). We are sure that you will enjoy this book and will profit with the technical and scientific contents. To finish, we are thankful to all of those who contributed to this book and who made it possible.info:eu-repo/semantics/publishedVersio

Graph Pattern Matching on Symmetric Multiprocessor Systems

Graph-structured data can be found in nearly every aspect of today's world, be it road networks, social networks or the internet itself. From a processing perspective, finding comprehensive patterns in graph-structured data is a core processing primitive in a variety of applications, such as fraud detection, biological engineering or social graph analytics. On the hardware side, multiprocessor systems, that consist of multiple processors in a single scale-up server, are the next important wave on top of multi-core systems. In particular, symmetric multiprocessor systems (SMP) are characterized by the fact, that each processor has the same architecture, e.g. every processor is a multi-core and all multiprocessors share a common and huge main memory space. Moreover, large SMPs will feature a non-uniform memory access (NUMA), whose impact on the design of efficient data processing concepts should not be neglected. The efficient usage of SMP systems, that still increase in size, is an interesting and ongoing research topic. Current state-of-the-art architectural design principles provide different and in parts disjunct suggestions on which data should be partitioned and or how intra-process communication should be realized. In this thesis, we propose a new synthesis of four of the most well-known principles Shared Everything, Partition Serial Execution, Data Oriented Architecture and Delegation, to create the NORAD architecture, which stands for NUMA-aware DORA with Delegation. We built our research prototype called NeMeSys on top of the NORAD architecture to fully exploit the provided hardware capacities of SMPs for graph pattern matching. Being an in-memory engine, NeMeSys allows for online data ingestion as well as online query generation and processing through a terminal based user interface. Storing a graph on a NUMA system inherently requires data partitioning to cope with the mentioned NUMA effect. Hence, we need to dissect the graph into a disjunct set of partitions, which can then be stored on the individual memory domains. This thesis analyzes the capabilites of the NORAD architecture, to perform scalable graph pattern matching on SMP systems. To increase the systems performance, we further develop, integrate and evaluate suitable optimization techniques. That is, we investigate the influence of the inherent data partitioning, the interplay of messaging with and without sufficient locality information and the actual partition placement on any NUMA socket in the system. To underline the applicability of our approach, we evaluate NeMeSys against synthetic datasets and perform an end-to-end evaluation of the whole system stack on the real world knowledge graph of Wikidata