Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.

Object-oriented database management systems (OODBMS) are expected to serve advanced application domains such as engineering design, office information systems, imaging systems, and multimedia. This book, based on a NATO Advanced Research Workshop, covers all aspects of object-oriented database systems from design principles to implementation of prototypes. Topics covered include model concepts, query optimization, query languages, functional programming formalism, storage systems, transaction models, interoperability, distributed computing, rule languages, open architectures, hypermedia systems, and many others. Designers and developers will benefit from the comprehensive presentation of the various modules of such systems, while practitioners will find examples of implemented prototypes.

Many applications process high volumes of streaming data, among them Internet traffic analysis, financial tickers, and transaction log mining. In general, a data stream is an unbounded data set that is produced incrementally over time, rather than being available in full before its processing begins. In this lecture, we give an overview of recent research in stream processing, ranging from answering simple queries on high-speed streams to loading real-time data feeds into a streaming warehouse for off-line analysis. We will discuss two types of systems for end-to-end stream processing: Data Stream Management Systems (DSMSs) and Streaming Data Warehouses (SDWs). A traditional database management system typically processes a stream of ad-hoc queries over relatively static data. In contrast, a DSMS evaluates static (long-running) queries on streaming data, making a single pass over the data and using limited working memory. In the first part of this lecture, we will discuss research problems in DSMSs, such as continuous query languages, non-blocking query operators that continually react to new data, and continuous query optimization. The second part covers SDWs, which combine the real-time response of a DSMS by loading new data as soon as they arrive with a data warehouse's ability to manage Terabytes of historical data on secondary storage. Table of Contents: Introduction / Data Stream Management Systems / Streaming Data Warehouses / Conclusions

Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.

This revised and expanded edition of Encyclopedia of Database Systems provides easy access to crucial concepts relevant to all aspects of very large databases, data management, and database systems, including areas of current interest and research results of historical significance. This comprehensive reference is organized alphabetically and each entry presents basic terminology, concepts, methods and algorithms, key results to date, references to the literature, and cross-references to other entries. Topics for the encyclopedia-including areas of current interest as well as research results of historical significance-were selected by a distinguished international advisory board and written by world-class experts in the field. New entries that reflect recent developments and technological advances in very large databases include: big data, big data technology, cloud computing, cloud data centers, business analytics, social networks, ranking, trust management, query over encrypted data, and more. Entirely new entries include database systems, relational database systems, databases, multimedia databases, bioinformatics, workflow systems, and web data management. Encyclopedia of Database Systems, 2nd edition, is designed to meet the needs of researchers, professors, graduate and undergraduate students in computer science and engineering. Industry professionals, from database specialists to software developers, will also benefit from this valuable reference work.