Supporting the software testing process through specification animation

Achieving consistency between a specification and its implementation is an important part of software development. In this paper, we present a method for generating passive test oracles that act as self-checking implementations. The implementation is verified using an animation tool to check that the behavior of the implementation matches the behavior of the specification. We discuss how to integrate this method into a framework developed for systematically animating specifications, which means a tester can significantly reduce testing time and effort by reusing work products from the animation. One such work product is a testgraph: a directed graph that partially models the states and transitions of the specification. Testgraphs are used to generate sequences for animation, and during testing, to execute these same sequences on the implementation.

Developing relational navigation to effectively understand software

Effective comprehension of complex software systems requires understanding of both the individual documents that represent software and the complex relationships that exist within and between documents. Relationships of all kinds play a vital role in a software engineer's comprehension of, and navigation within and between, software documents. User-determined relationships have the additional role of enabling the engineer to create and maintain relational documentation that cannot be generated by tools or derived from other relationships. We argue that for a software development environment to effectively support the understanding of complex software systems, relational navigation must be supported at both the document-focused (intra-document) and relation-focused (inter-document) levels. The need for a relation-focused approach is highlighted by an evaluation of an existing document-focused relational interface. We conclude with the requirements for a relation-focused approach to relational navigation. These requirements focus on the user's perspective when interacting with a collection of related documents. We define the requirements for a software development environment that effectively supports the understanding of the software documents and relationships that define a complex software system.

Specification matching of object-oriented components

Object-orientation supports software reuse via features such as abstraction, information hiding, polymorphism, inheritance and redefinition. However, while libraries of classes do exist, one of the challenges that still remains is to locate suitable classes and adapt them to meet the specific requirements of the software developer. Traditional approaches to library retrieval are text-based; it is therefore difficult for the developer to express their requirements in a precise and unambiguous manner. A more promising approach is specification-based retrieval, where library component interfaces and requirements are expressed using a formal specification language. In this case retrieval is based on matching formal specifications. In this paper we describe how existing approaches to specification matching can be extended to handle object-oriented components.

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

Further results on the relationship between mu-invariant measures and quasi-stationary distributions for absorbing continuous-time Markov chains

This note considers continuous-time Markov chains whose state space consists of an irreducible class, C, and an absorbing state which is accessible from C. The purpose is to provide results on mu-invariant and mu-subinvariant measures where absorption occurs with probability less than one. In particular, the well-known premise that the mu-invariant measure, m, for the transition rates be finite is replaced by the more natural premise that m be finite with respect to the absorption probabilities. The relationship between mu-invariant measures and quasi-stationary distributions is discussed. (C) 2000 Elsevier Science Ltd. All rights reserved.

New methods for determining quasi-stationary distributions for Markov chains

We shall be concerned with the problem of determining quasi-stationary distributions for Markovian models directly from their transition rates Q. We shall present simple conditions for a mu-invariant measure m for Q to be mu-invariant for the transition function, so that if m is finite, it can be normalized to produce a quasi-stationary distribution. (C) 2000 Elsevier Science Ltd. All rights reserved.

Modelling solute transport in structured soils: Performance evaluation of the ADR and TRM models

The movement of chemicals through the soil to the groundwater or discharged to surface waters represents a degradation of these resources. In many cases, serious human and stock health implications are associated with this form of pollution. The chemicals of interest include nutrients, pesticides, salts, and industrial wastes. Recent studies have shown that current models and methods do not adequately describe the leaching of nutrients through soil, often underestimating the risk of groundwater contamination by surface-applied chemicals, and overestimating the concentration of resident solutes. This inaccuracy results primarily from ignoring soil structure and nonequilibrium between soil constituents, water, and solutes. A multiple sample percolation system (MSPS), consisting of 25 individual collection wells, was constructed to study the effects of localized soil heterogeneities on the transport of nutrients (NO3-, Cl-, PO43-) in the vadose zone of an agricultural soil predominantly dominated by clay. Very significant variations in drainage patterns across a small spatial scale were observed tone-way ANOVA, p < 0.001) indicating considerable heterogeneity in water flow patterns and nutrient leaching. Using data collected from the multiple sample percolation experiments, this paper compares the performance of two mathematical models for predicting solute transport, the advective-dispersion model with a reaction term (ADR), and a two-region preferential flow model (TRM) suitable for modelling nonequilibrium transport. These results have implications for modelling solute transport and predicting nutrient loading on a larger scale. (C) 2001 Elsevier Science Ltd. All rights reserved.

A family of perfect hashing methods

Minimal perfect hash functions are used for memory efficient storage and fast retrieval of items from static sets. We present an infinite family of efficient and practical algorithms for generating order preserving minimal perfect hash functions. We show that almost all members of the family construct space and time optimal order preserving minimal perfect hash functions, and we identify the one with minimum constants. Members of the family generate a hash function in two steps. First a special kind of function into an r-graph is computed probabilistically. Then this function is refined deterministically to a minimal perfect hash function. We give strong theoretical evidence that the first step uses linear random time. The second step runs in linear deterministic time. The family not only has theoretical importance, but also offers the fastest known method for generating perfect hash functions.

Supporting contexts in program refinement

A program can be refined either by transforming the whole program or by refining one of its components. The refinement of a component is, for the main part, independent of the remainder of the program. However, refinement of a component can depend on the context of the component for information about the variables that are in scope and what their types are. The refinement can also take advantage of additional information, such as any precondition the component can assume. The aim of this paper is to introduce a technique, which we call program window inference, to handle such contextual information during derivations in the refinement calculus. The idea is borrowed from a technique, called window inference, for handling context in theorem proving. Window inference is the primary proof paradigm of the Ergo proof editor. This tool has been extended to mechanize refinement using program window inference. (C) 1997 Elsevier Science B.V.