An XML Query Engine for Network-Bound Data

XML has become the lingua franca for data exchange and integration across administrative and enterprise boundaries. Nearly all data providers are adding XML import or export capabilities, and standard XML Schemas and DTDs are being promoted for all types of data sharing. The ubiquity of XML has removed one of the major obstacles to integrating data from widely disparate sources –- namely, the heterogeneity of data formats. However, general-purpose integration of data across the wide area also requires a query processor that can query data sources on demand, receive streamed XML data from them, and combine and restructure the data into new XML output -- while providing good performance for both batch-oriented and ad-hoc, interactive queries. This is the goal of the Tukwila data integration system, the first system that focuses on network-bound, dynamic XML data sources. In contrast to previous approaches, which must read, parse, and often store entire XML objects before querying them, Tukwila can return query results even as the data is streaming into the system. Tukwila is built with a new system architecture that extends adaptive query processing and relational-engine techniques into the XML realm, as facilitated by a pair of operators that incrementally evaluate a query’s input path expressions as data is read. In this paper, we describe the Tukwila architecture and its novel aspects, and we experimentally demonstrate that Tukwila provides better overall query performance and faster initial answers than existing systems, and has excellent scalability

Survey of NoSQL Database Engines for Big Data

Cloud computing is a paradigm shift that provides computing over Internet. With growing outreach of Internet in the lives of people, everyday large volume of data is generated from different sources such as cellphones, electronic gadgets, e-commerce transactions, social media, and sensors. Eventually, the size of generated data is so large that it is also referred as Big Data. Companies harvesting business opportunities in digital world need to invest their budget and time to scale their IT infrastructure for the expansion of their businesses. The traditional relational databases have limitations in scaling for large Internet scale distributed systems. To store rapidly expanding high volume Big Data efficiently, NoSQL data stores have been developed as an alternative solution to the relational databases. The purpose of this thesis is to provide a holistic overview of different NoSQL data stores. We cover different fundamental principles supporting the NoSQL data store development. Many NoSQL data stores have specific and exclusive features and properties. They also differ in their architecture, data model, storage system, and fault tolerance abilities. This thesis describes different aspects of few NoSQL data stores in detail. The thesis also covers the experiments to evaluate and compare the performance of different NoSQL data stores on a distributed cluster. In the scope of this thesis, HBase, Cassandra, MongoDB, and Riak are four NoSQL data stores selected for the benchmarking experiments

Construction, Application and Analysis of the Oligonucleotide Database, Viroligo

Biochemistry and Molecular Biolog

Language constructs for managing change in process-centered environments

Change is pervasive during software development, af-fecting objects, processes, and environments. In pro-cess centered environments, change management can be facilitated by software-process programming, which for-malizes the representation of software products and pro-cesses using software-process programming languages (SPPLs). To fully realize this goal SPPLs should in-clude constructs that specifically address the problems of change management. These problems include lack of representation of inter-object relationships, weak se-mantics for inter-object relationships, visibility of im-plementations, lack of formal representation of soft-ware processes, and reliance on programmers to manage change manually

Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes

Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS™ as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP® with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave® assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information

Division of Research and Economic Development Annual Report for FY2002

Annual report for the Division of Research and Economic Development of the University of Rhode Island for the year 2001-2002. Includes statistics of project proposals, expenditures, URI Foundation Awards, previous annual report summaries and awards received by individual academic and administrative departments

Proceedings of the University Alliance Executive Directors Workshop - ECIS 2001

The introduction of Enterprise Systems (ES) into the curriculum at Business and IS Faculties and Schools is for many universities a major challenge. However, this problem is in various aspects of special nature: the students' demand is enormous and in many cases product-focused, Enterprise Systems are typically very comprehensive and complex, and knowledge about ES is often missing. By the time textbooks of satisfying quality are available, there are new systems' upgrades and innovation cycles to deal with. The Queensland University of Technology (QUT) is comprehensively using the market leading Enterprise System SAP R/3 within its curriculum and is also conducting research in this area. This paper briefly reports on the activities and experiences at QUT, which is now one of the few world-wide mySAP University Application Hosting Centers.<br/

Mechanisms underlying postnatal development of primary somatosensory cortex

Layer IV of the mouse somatosensory cortex contains discrete cytoarchitectonic units called 'barrels', formed in response to thalamocortical axon invasion by two processes: translocation of cortical cells to form a cell-dense barrel wall and cell-sparse barrel hollow, and selective dendritic elaboration toward thalamocortical afferents to form oriented dendritic branch patterns. Interestingly gene knockout of several members of the N-Methyl-D-Aspartate (NMDA) receptor -complex (NRC) disrupts barrel formation, indicating that synaptic activity is critical for barrel formation. Little is known of the cellular processes initiated by glutamate receptor activation; however, recent evidence suggests an interaction between neuronal activity and Wnt signalling. Wnts are secreted glycoproteins, are powerful regulators of cell proliferation and differentiation, and their signalling pathway involves proteins that directly participate in both gene transcription and cell adhesion. Wnt7a and Dv11 knockout mice exhibit delays in glomerular rosette formation; a cerebellar structure similar to barrels whose development involves granule cell migration and dendritic rearrangement. Furthermore activity dependent Wnt release can regulate the enhancement of dendrite arborisation, raising the possibility that NRC components and Wnts may interact to regulate barrel development.Recent findings suggest that membrane association guanylyl kinases (MAGUKs) may be the key scaffolding molecules that mediate the interaction between glutamate receptor and Wnt signalling pathways. The MAGUK family includes Postsynaptic Density (PSD)-95 and Synapse Associated Protein (SAP)-102, two key molecules of the NRC during barrel formation. These MAGUKs also bind the Wnt receptor family Frizzled and SAP-102 binds to APC, a key Frizzled-signalling protein. As a first step in examining a role for Wnts in barrel formation, the gene expression patterns of members of the Wnt, Frizzleds and secreted Frizzled related protein (sFRPs) families during barrel cortex development were measured using degenerate primer RT-PCR, quantitative real-time PCR and in-situ hybridization. Wnts 2b, 3, 4, 5a, la, 7b, 9a, 11, 16 were found in the barrel cortex, suggesting that these members of the Wnt family may play a role in barrel development, and Wnt7b, Frizzled 4, Frizzled 9, and Frizzled 3 were conspicuously downregulated in mutant mice that lack barrels, namely Plc-ß1⁻/⁻, Pkar2ß⁻/⁻ and Mglur5⁻/⁻ mice.In order to determine whether Wnts, members of the Wnt signaling machinery and MAGUKs associated with Wnt signaling are essential for barrel formation, the barrel phenotype of all available postnatally viable Wnt gene knockouts, Wnt2b⁻/⁻, Wnt7a⁻/⁻, Wnt8b⁻/⁻, Wnt signaling component knockouts Dvl⁻/⁻, MAGUK knockouts Sap-102'1', Psd-95'1' and double knockouts of Wnt7a"Dvr'~ and of Sap-102⁻/⁻Psd-95⁻/⁻ were examined. Barrels appeared normal in all mutants, apart from compound Sap-102⁻/⁻Psd-95⁻/⁻ and Sap-102⁻/⁻Psd-95⁻/⁻ mice, which exhibited poorer barrel segregation compared to wild type.In order to achieve a detailed understanding of the mechanisms by which neuronal activity regulates barrel development, we need a detailed understanding of the intracellular pathways activated by NMDA receptors during development. In searching the literature, data concerning the developmental expression patterns of NRC components can be difficult to locate, as the prevailing database tools used either search only title, author and keyword abstract text (NCBI PubMed) potentially missing desired information, or as in the unique case of Google Scholar, search the full text of electronically published papers, but yield overwhelming numbers of results in the process.The Jackson Laboratories MGI suite offers an impressive way of mining the literature for such data, but the content is sparse, relying on author submission and attempting to map expression throughout the whole mouse. For example, the only gene present in MGI for postnatal layer IV cerebral cortex is Apc2.In order to bring together the data in the literature and from the mouse genome projects into a usable and accessible way, we decided to create a web-based centralised resource for the developmental neuroscience community, containing expression profiles of NRC components within mouse somatosensory cortex. By performing exhaustive literature searches utilising Google Scholar and PubMed, and linking to sequence and mutant mouse availability information elsewhere, BGI offers a portal for such information and also offers a forum for the notification of unpublished observations of transgenic animals displaying normal barrel formation, preventing duplication of experiments. Barrelgene.info should provide a key resource for any researcher interested in the molecular basis of cortical development