A Foolish Consistency: Technical Challenges in Consistency Management

Abstract. This paper outlines the area of consistency management and ar-gues for its importance. A motivating example is presented to support the argument. The paper sets out the key technical challenges for research in this area. A broad research agenda is outlined with some signposting of par-ticularly interesting directions. 1 What is Consistency Management? "A foolish consistency is the hobgoblin of little minds adored by little statesmen and philosophers and divines. With consistency a great soul has simply nothing to do... speak what you think today in words as hard as cannonballs and tomorrow speak what tomorrow thinks in hard words again though it contradict everything you said today" R.W. Emerson The everyday concept of inconsistency is easy to grasp. It is simply saying something in one place and another contradictory thing in another place. The equivalent of the standard logical notion of inconsistency in which one asserts both that the sky is blu

Better bioinformatics through usability analysis

Motivation: Improving the usability of bioinformatics resources enables researchers to find, interact with, share, compare and manipulate important information more effectively and efficiently. It thus enables researchers to gain improved insights into biological processes with the potential, ultimately, of yielding new scientific results. Usability ‘barriers' can pose significant obstacles to a satisfactory user experience and force researchers to spend unnecessary time and effort to complete their tasks. The number of online biological databases available is growing and there is an expanding community of diverse users. In this context there is an increasing need to ensure the highest standards of usability. Results: Using ‘state-of-the-art' usability evaluation methods, we have identified and characterized a sample of usability issues potentially relevant to web bioinformatics resources, in general. These specifically concern the design of the navigation and search mechanisms available to the user. The usability issues we have discovered in our substantial case studies are undermining the ability of users to find the information they need in their daily research activities. In addition to characterizing these issues, specific recommendations for improvements are proposed leveraging proven practices from web and usability engineering. The methods and approach we exemplify can be readily adopted by the developers of bioinformatics resources. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Foreword:2nd workshop [email protected]

The 2nd edition of the Workshop [email protected] was held at the 19th International Conference on Requirements Engineering (RE 2011) in the city of Trento, Italy on the 30th of August 2011. It was organized by Nelly Bencomo, Emmanuel Letier, Jon Whittle, Anthony Finkelstein, and Kris Welsh. This foreword presents a digest of the discussions and presentations that took place during the workshop

Foreword:first workshop [email protected]

The first edition of the Workshop [email protected] was held at the Eighteenth International Conference on Requirements Engineering (RE 2010) in the city of Sydney, NSW, Australia on the 28th of September 2010. It was organized by Pete Sawyer, Jon Whittle, Nelly Bencomo, Daniel Berry, and Anthony Finkelstein. This foreword presents a digest of the presentations and discussions that took place during the workshop

Semantic web data warehousing for caGrid

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data models exposed on caGrid are semantically well annotated, it is currently up to the caGrid client to infer relationships between the different models and their classes. In this paper, we present a Semantic Web-based data warehouse (Corvus) for creating relationships among caGrid models. This is accomplished through the transformation of semantically-annotated caBIG® Unified Modeling Language (UML) information models into Web Ontology Language (OWL) ontologies that preserve those semantics. We demonstrate the validity of the approach by Semantic Extraction, Transformation and Loading (SETL) of data from two caGrid data sources, caTissue and caArray, as well as alignment and query of those sources in Corvus. We argue that semantic integration is necessary for integration of data from distributed web services and that Corvus is a useful way of accomplishing this. Our approach is generalizable and of broad utility to researchers facing similar integration challenges

Using JULE to generate a compliance test suite for the UML standard

The Java-UML Lightweight Enumerator (JULE) tool implements a vitally important aspect of the framework for software tool certification- test suite generation. The framework uses UML models as the test inputs for the bounded exhaustive-testing approach. Within a size bound for the metamodel types, JULE enumerates only the set of non-isomorphic models in the form of relational structures. These models are classified into two sets- demonstration and counterexample- using Binary Decision Diagrams (BDDs). The power of JULE lies in its model enumeration and its use of a high-performance grid infrastructure. Hence, JULE efficiently generates a very small test suite while increasing the bound on the input size to the extent that is practical for certification purpose

Implementing a compliance manager

Many companies claim to adhere to standards for software project development. This is often used as a marketing tool when eliciting business. But how does the customer or project manager know that these standards are being completely and consistently applied in their projects? In the paper ’Managing Standards Compliance’, we identify this problem and describe a support environment to provide identification and correction of non-compliance to standards. This paper details the experiences gained while implementing such a tolerant support system

Exploring the evidence base for national and regional policy interventions to combat resistance

The effectiveness of existing policies to control antimicrobial resistance is not yet fully understood. A strengthened evidence base is needed to inform effective policy interventions across countries with different income levels and the human health and animal sectors. We examine three policy domains—responsible use, surveillance, and infection prevention and control—and consider which will be the most effective at national and regional levels. Many complexities exist in the implementation of such policies across sectors and in varying political and regulatory environments. Therefore, we make recommendations for policy action, calling for comprehensive policy assessments, using standardised frameworks, of cost-effectiveness and generalisability. Such assessments are especially important in low-income and middle-income countries, and in the animal and environmental sectors. We also advocate a One Health approach that will enable the development of sensitive policies, accommodating the needs of each sector involved, and addressing concerns of specific countries and regions