41129929
The Atomic Manifesto
This paper is a manifesto for future research on "atomicity" in its many guises and is based on a five-day workshop on "Atomicity in System Design and Execution" that took place in Schloss Dagstuhl in Germany in April 2004.
15308825
Scientific Decisions which Characterize VDM
The formal description and development method known as VDM has been used extensively, its specification language is now an ISO standard, and it has influenced other specification languages. The origins of VDM are normally placed in language description or semantics but it is probably best known in the wider arena of formal methods for (general) program specification and design. This paper sets out a personal view of some of the key technical decisions which characterize the Vienna Development Method.
6772552
Fixing the semantics of some concurrent object-oriented concepts
Abstract Concurrent object-oriented languages provide a suitable target for a compositional design process that copes with the interference inherent with concurrency. Fixing the semantics of an object-based design language has been undertaken using structured operational semantics and by a mapping to the pi-calculus. These two approaches are outlined and contrasted. In particular, the difficulties in the two approaches of justifying the proof rules of the proposed design method are explained.
45828501
Formal Definition in Program Development
The intent of the current paper is to show how a large problem like compiler development can be divided in a way which provides a structure for arguments of correctness. Although mechanically checked proofs are not envisaged, the use of formal notation is recommended so that the basis for correctness arguments exists.
9236653
The Early Search for Tractable Ways of Reasoning about Programs
This article traces the history - up to around 1990 - of research on reasoning about programs. The main focus is on sequential imperative programs but some comments are made on concurrency. The main thesis is that the idea of reasoning about programs has been around since they were first written; the search has been to find tractable methods.
2399941
Operational semantics: Concepts and their expression
6251055
End-User Programming
End-user software development is a growing avocation in every industry and every country. By the middle of the next century, computer literacy and programming skills will be almost as common as reading and writing skills. Almost every knowledge worker in the world will be able to program if he or she sets out to do so. The implications of widespread end-user software are only just beginning to be considered. There are many exciting possibilities and some potential hazards. The time is now at hand to consider business topics such as ownership of end-user applications and liability in cases of significant errors. >
36993113
A Collaborative Schema Integration System
Conceptual modelling as applied to database development can be described as a two stage process: schema modelling followed by schema integration. Schema modelling is the process of transforming individual user requirements into a conceptual schema: an implementation-independent map of data requirements. Schema integration is the process of combining individual conceptual schemas into a single, unified schema. Single-user tools for schema modelling have enjoyed much success partly because the process of schema modelling has become relatively well formalised. Although a number of formal approaches to conducting schema integration have been proposed, it appears that schema integration tools have not enjoyed the same level of success. This we attribute not so much to the problem of formalisation but to the inherent collaborative nature of schema integration work. This paper first discusses the importance of collaboration to schema integration work. It then describes SISIBIS, a demonstrator system employing the IBIS (Issue Based Information System) scheme to support collaborative database design.
26658779
Virtual architecture based on a binary relational model: A museum hypermedia application
32895841
Software Change Management
Software projects change rapidly, which makes efficient change management a major challenge for the software industry. This challenge was poorly met for years because of rudimentary tools. The paper considers how modern change management, or configuration control tools must encompass changes affecting every kind of software deliverable and artifact.
11309996
Automated methods of predicting the function of biological sequences using GO and BLAST
BackgroundWith the exponential increase in genomic sequence data there is a need to develop automated approaches to deducing the biological functions of novel sequences with high accuracy. Our aim is to demonstrate how accuracy benchmarking can be used in a decision-making process evaluating competing designs of biological function predictors. We utilise the Gene Ontology, GO, a directed acyclic graph of functional terms, to annotate sequences with functional information describing their biological context. Initially we examine the effect on accuracy scores of increasing the allowed distance between predicted and a test set of curator assigned terms. Next we evaluate several annotator methods using accuracy benchmarking. Given an unannotated sequence we use the Basic Local Alignment Search Tool, BLAST, to find similar sequences that have already been assigned GO terms by curators. A number of methods were developed that utilise terms associated with the best five matching sequences. These methods were compared against a benchmark method of simply using terms associated with the best BLAST-matched sequence (best BLAST approach).ResultsThe precision and recall of estimates increases rapidly as the amount of distance permitted between a predicted term and a correct term assignment increases. Accuracy benchmarking allows a comparison of annotation methods. A covering graph approach performs poorly, except where the term assignment rate is high. A term distance concordance approach has a similar accuracy to the best BLAST approach, demonstrating lower precision but higher recall. However, a discriminant function method has higher precision and recall than the best BLAST approach and other methods shown here.ConclusionAllowing term predictions to be counted correct if closely related to a correct term decreases the reliability of the accuracy score. As such we recommend using accuracy measures that require exact matching of predicted terms with curator assigned terms. Furthermore, we conclude that competing designs of BLAST-based GO term annotators can be effectively compared using an accuracy benchmarking approach. The most accurate annotation method was developed using data mining techniques. As such we recommend that designers of term annotators utilise accuracy benchmarking and data mining to ensure newly developed annotators are of high quality.