Roger G. Johnson

Extending relational algebra to manipulate temporal data

Abstract Some weaknesses of relational algebra when manipulating temporal data are identified. An extension of this algebra is described, which helps overcome the problems. The proposed model is simple in structure, powerful and its operational capabilities are readily understandable by the user. In addition, an experimental implementation is described.

A dynamic runtime coupling metric for meta-level architectures

The extent of coupling in an object-oriented system has implications for its quality in terms of software maintenance. In turn, the extent of reuse in a software system also has implications for the maintainability of that system. One important feature of reflective systems is their dynamic behaviour. In such systems, objects exchange coupling interactions to a larger degree than corresponding static systems providing the same functionality. In this paper, we look at object coupling as it evolves during program execution and propose a measure which takes object interactions into account. The measure can be used to compare systems built on meta-level architectures with systems having no reflective features yet, at the same time, exhibiting the same interface.

Dynamic coupling metric: proof of concept

Most object-oriented coupling measures proposed in the literature deal with coupling at the static class level. Measuring dynamic object coupling however gives potential for greater insight into system structure and comparison of the architectural aspects of different systems. In previous work, a dynamic coupling metric (DCM) was introduced and validated theoretically. The authors investigate an empirical validation of this metric. A tool was developed to collect dynamic coupling data represented by message exchanges between objects at runtime; two system models with different architectural characteristics providing the same functionality were then considered. Empirical validation of the metric showed it to be a useful vehicle for comparing the runtime coupling characteristics of software systems. Results also showed that for examples covering various types of couplings, object-oriented (OO) reflective systems separating the base level from the meta-level exhibited significantly less coupling when compared with corresponding systems with a traditional OO (single-level) architecture.

An Extension of the Relational Model to Support Generic Intervals

A consistent extension of the relational model is defined, which allows the recording and manipulation of generic intervals. Two new relational algebra operations are defined, which are closed. The proposed model has a wide range of applications areas, such as engineering, CAD, cartography, version modelling, temporal databases, soil information systems, mathematics, the management of spatial data and many others.

PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources

MOTIVATION The PFDB (Protein Family Database) is a new database designed to integrate protein family-related data with relevant functional and genomic data. It currently manages biological data for three projects-the CATH protein domain database (Orengo et al., 1997; Pearl et al., 2001), the VIDA virus domains database (Albà et al., 2001) and the Gene3D database (Buchan et al., 2001). The PFDB has been designed to accommodate protein families identified by a variety of sequence based or structure based protocols and provides a generic resource for biological research by enabling mapping between different protein families and diverse biochemical and genetic data, including complete genomes. RESULTS A characteristic feature of the PFDB is that it has a number of meta-level entities (for example aggregation, collection and inclusion) represented as base tables in the final design. The explicit representation of relationships at the meta-level has a number of advantages, including flexibility-both in terms of the range of queries that can be formulated and the ability to integrate new biological entities within the existing design. A potential drawback with this approach-poor performance caused by the number of joins across meta-level tables-is avoided by implementing the PFDB with materialized views using the mature relational database technology of Oracle 8i. The resultant database is both fast and flexible. This paper presents the principles on which the database has been designed and implemented, and describes the current status of the database and query facilities supported.

Joining nested relations and subrelations

Abstract This paper proposes a generalisation of the “natural” join operation which is shown to be applicable to all joinable nested relations. The “natural” join operation can be applied to any pair of relations which have one or more attributes in common even when they are in different subrelations and at different nesting levels in each relation; it is not just executing a join between specific user-defined attributes. This paper systematically reviews the varied forms of joins between nested relations and subrelations. The generalisation of join uses one or more of the six distinct cases of the join operation applied to nested relations which are identified later in the paper, distinguished by certain properties of the attributes in the join paths between the relations that participate in the join operation. These properties depend on whether an attribute is either atomic or relation-valued and on whether it is at either the top level or lower levels (same or different) of the two relations.

Some comments on the use of ambiguous decision tables and their conversion to computer programs

This paper comments upon recently published work on decision table translation using methods similar to the rule-mask technique. The applicability of these methods under various possible conventions on overall table meaning is discussed, and it is argued that there is a place both for the multi-rule and the single-rule (or action set) convention in decision table usage.

Applications of dynamic proxies in distributed environments

In object‐oriented programming (OOP), proxies are entities that act as an intermediary between client objects and target objects. Dynamic proxies can be used to construct distributed systems that support the open implementation approach and promote code reuse. The OO paradigm supports code reuse through various ways including inheritance, polymorphism and aggregation. In this paper, we adopt a definition of software reuse restricted to reuse of code components and address the question of constructing distributed systems based on dynamic proxies. Different networking techniques and programming paradigms such as Javas Remote Method Invocation (RMI), the Common Object Request Broker Architecture (CORBA) and Java Servlets are used to implement the distributed client/server architecture. Copyright

Soft computing for intelligent data analysis

Intelligent data analysis (IDA) is an interdisciplinary study concerned with the effective analysis of data. The paper briefly looks at some of the key issues in intelligent data analysis, discusses the opportunities for soft computing in this context, and presents several IDA case studies in which soft computing has played key roles. These studies are all concerned with complex real-world problem solving, including consistency checking between mass spectral data with proposed chemical structures, screening for glaucoma and other eye diseases, forecasting of visual field deterioration, and diagnosis in an oil refinery involving multivariate time series. Bayesian networks, evolutionary computation, neural networks, and machine learning in general are some of those soft computing techniques effectively used in these studies.

DBJ - a dynamic balancing hash join algorithm in multiprocessor database systems

The Dynamic Balancing Hash Join (DBJ), has been proposed to handle the problem of skewed data in the join operation in multiprocessor database systems. The objective of this new algorithm is to avoid the high cost of preprocessing inherent in existing algorithms. The new algorithm only redistributes a small portion of the partitioned data and, thereby achieves a balanced output with little extra cost. This is achieved dynamically, without knowledge of the input distribution, nor any co-ordinating processor. A performance analysis shows that the new algorithm performs better than existing balancing hash join algorithms for a wide degree of skew.