Automatic optimization of array queries

Non-trivial scientific applications often involve complex computations on large multi-dimensional datasets. Using relational database technology for these datasets is cumbersome since expressing the computations in terms of relational queries is difficult and time-consuming. Moreover, query optimization strategies successful in classical relational domains may not suffice when applied to the multi-dimensional array domain. The RAM (Relational Array Mapping) system hides these issues by providing a transparent mapping between the scientific problem specification and the underlying database system. This paper focuses on the RAM query optimizer which is specifically tuned to exploit the characteristics of the array paradigm. We detail how an intermediate array-algebra and several equivalence rules are used to create efficient query plans and how, with minor extensions, the optimizer can automatically parallelize array operation

User Defined Types and Nested Tables in Object Relational Databases

Bernadette Byrne, Mary Garvey, ‘User Defined Types and Nested Tables in Object Relational Databases’, paper presented at the United Kingdom Academy for Information Systems 2006: Putting Theory into Practice, Cheltenham, UK, 5-7 June, 2006.There has been much research and work into incorporating objects into databases with a number of object databases being developed in the 1980s and 1990s. During the 1990s the concept of object relational databases became popular, with object extensions to the relational model. As a result, several relational databases have added such extensions. There has been little in the way of formal evaluation of object relational extensions to commercial database systems. In this work an airline flight logging system, a real-world database application, was taken and a database developed using a regular relational database and again using object relational extensions, allowing the evaluation of the relational extensions.Peer reviewe

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions

Moa and the multi-model architecture: a new perspective on XNF2

Advanced non-traditional application domains such as geographic information systems and digital library systems demand advanced data management support. In an effort to cope with this demand, we present the concept of a novel multi-model DBMS architecture which provides evaluation of queries on complexly structured data without sacrificing efficiency. A vital role in this architecture is played by the Moa language featuring a nested relational data model based on XNF2, in which we placed renewed interest. Furthermore, extensibility in Moa avoids optimization obstacles due to black-box treatment of ADTs. The combination of a mapping of queries on complexly structured data to an efficient physical algebra expression via a nested relational algebra, extensibility open to optimization, and the consequently better integration of domain-specific algorithms, makes that the Moa system can efficiently and effectively handle complex queries from non-traditional application domains

Deliverable DJRA1.2. Solutions and protocols proposal for the network control, management and monitoring in a virtualized network context

This deliverable presents several research proposals for the FEDERICA network, in different subjects, such as monitoring, routing, signalling, resource discovery, and isolation. For each topic one or more possible solutions are elaborated, explaining the background, functioning and the implications of the proposed solutions.This deliverable goes further on the research aspects within FEDERICA. First of all the architecture of the control plane for the FEDERICA infrastructure will be defined. Several possibilities could be implemented, using the basic FEDERICA infrastructure as a starting point. The focus on this document is the intra-domain aspects of the control plane and their properties. Also some inter-domain aspects are addressed. The main objective of this deliverable is to lay great stress on creating and implementing the prototype/tool for the FEDERICA slice-oriented control system using the appropriate framework. This deliverable goes deeply into the definition of the containers between entities and their syntax, preparing this tool for the future implementation of any kind of algorithm related to the control plane, for both to apply UPB policies or to configure it by hand. We opt for an open solution despite the real time limitations that we could have (for instance, opening web services connexions or applying fast recovering mechanisms). The application being developed is the central element in the control plane, and additional features must be added to this application. This control plane, from the functionality point of view, is composed by several procedures that provide a reliable application and that include some mechanisms or algorithms to be able to discover and assign resources to the user. To achieve this, several topics must be researched in order to propose new protocols for the virtual infrastructure. The topics and necessary features covered in this document include resource discovery, resource allocation, signalling, routing, isolation and monitoring. All these topics must be researched in order to find a good solution for the FEDERICA network. Some of these algorithms have started to be analyzed and will be expanded in the next deliverable. Current standardization and existing solutions have been investigated in order to find a good solution for FEDERICA. Resource discovery is an important issue within the FEDERICA network, as manual resource discovery is no option, due to scalability requirement. Furthermore, no standardization exists, so knowledge must be obtained from related work. Ideally, the proposed solutions for these topics should not only be adequate specifically for this infrastructure, but could also be applied to other virtualized networks.Postprint (published version

Logic Programming Applications: What Are the Abstractions and Implementations?

This article presents an overview of applications of logic programming, classifying them based on the abstractions and implementations of logic languages that support the applications. The three key abstractions are join, recursion, and constraint. Their essential implementations are for-loops, fixed points, and backtracking, respectively. The corresponding kinds of applications are database queries, inductive analysis, and combinatorial search, respectively. We also discuss language extensions and programming paradigms, summarize example application problems by application areas, and touch on example systems that support variants of the abstractions with different implementations

Implementing imperfect information in fuzzy databases

Information in real-world applications is often vague, imprecise and uncertain. Ignoring the inherent imperfect nature of real-world will undoubtedly introduce some deformation of human perception of real-world and may eliminate several substantial information, which may be very useful in several data-intensive applications. In database context, several fuzzy database models have been proposed. In these works, fuzziness is introduced at different levels. Common to all these proposals is the support of fuzziness at the attribute level. This paper proposes first a rich set of data types devoted to model the different kinds of imperfect information. The paper then proposes a formal approach to implement these data types. The proposed approach was implemented within a relational object database model but it is generic enough to be incorporated into other database models.ou

TEMPOS: A Platform for Developing Temporal Applications on Top of Object DBMS

This paper presents TEMPOS: a set of models and languages supporting the manipulation of temporal data on top of object DBMS. The proposed models exploit object-oriented technology to meet some important, yet traditionally neglected design criteria related to legacy code migration and representation independence. Two complementary ways for accessing temporal data are offered: a query language and a visual browser. The query language, namely TempOQL, is an extension of OQL supporting the manipulation of histories regardless of their representations, through fully composable functional operators. The visual browser offers operators that facilitate several time-related interactive navigation tasks, such as studying a snapshot of a collection of objects at a given instant, or detecting and examining changes within temporal attributes and relationships. TEMPOS models and languages have been formalized both at the syntactical and the semantical level and have been implemented on top of an object DBMS. The suitability of the proposals with regard to applications' requirements has been validated through concrete case studies