730 research outputs found
A comparative study of process mediator components that support behavioral incompatibility
Most businesses these days use the web services technology as a medium to
allow interaction between a service provider and a service requestor. However,
both the service provider and the requestor would be unable to achieve their
business goals when there are miscommunications between their processes. This
research focuses on the process incompatibility between the web services and
the way to automatically resolve them by using a process mediator. This paper
presents an overview of the behavioral incompatibility between web services and
the overview of process mediation in order to resolve the complications faced
due to the incompatibility. Several state-of the-art approaches have been
selected and analyzed to understand the existing process mediation components.
This paper aims to provide a valuable gap analysis that identifies the
important research areas in process mediation that have yet to be fully
explored.Comment: 20 Pages, 9 figures and 8 Tables; International Journal on Web
Service Computing (IJWSC), September 2011, Volume 2, Number
Flooding-Based Algorithm for Behavioural Compatibility Measuring
Nowadays, large software systems are mostly built using existing services. These are not always designed to interact, i.e., their public interfaces often present some mismatches. Checking compatibility of service interfaces allows one to avoid erroneous executions when composing the services and ensures correct reuse and interaction. Service compatibility has been intensively studied, in particular for discovery purposes, but most of existing approaches return a Boolean result. In this paper, we present a quantitative approach for measuring the compatibility degree of service interfaces. Our method is generic and flooding-based, and fully automated by a prototype tool
A Component-Based Approach for Scientific Services for Education and Research (Scientific SEARCH)
Today’s challenge for retrieving digital information by users such as “students,” educators,” or “researchers” is coping, more than ever before, with the excessive data and information available. The problem is further compounded because of the way scientific knowledge is structured, in terms of expert interviews, articles, conference coverage, journal scans etc. Great progress has been made in digital library research. The NSF/NSDL through their initiatives has assembled a great set of tools and techniques that hold significant potential. Many projects are now underway applying these tools and techniques to meet the information needs of different user communities. The primary focus of Scientific SEARCH project is enhancing access to high quality learning materials and resources, modules, and other digital objects targeted towards scientific consumer and scientific producer. The project will use a multi-phased approach to achieve the objective. The paper describes the first-phase work submitted to NSF 04-542 solicitation
Landscape genomics of tropical high altitude plant species
Changes to species distributions involve demographic processes that occur over generations and affect allele frequencies within populations, leading to patterns of genetic restructuring. The specific genetic structuring patterns that will be observed as a consequence depend on explicit geographical features, such as topography and latitude. Over the first decades of phylogeography, the effect of climate history and geography on species genomes was examined at low resolution with DNA sequences and other traditional molecular markers. However, During the last five years it has become feasible to obtain genomic data for non-model organisms and large sample sizes.
The present thesis spans the transition years between phylogeographic studies being restricted to low resolution molecular markers, and new methods facilitating the generation of genomic data for non-model species. As such, this thesis focuses on two main points. First, on the methodological aspects of utilising double digest RAD-seq (ddRAD) for individual-based population genetics and phylogeography of plant species. Second, on applying the obtained data to examine one of the classic. but as yet not fully explained, biodiversity patterns: the biodiversity excess within tropical mountains.
The main contributions of this thesis at the methodological level are; (1) demonstrating the utility of DNA replicates for the estimation of genotyping error and optimisation of de novo assembly; (2) proposing a method for identifying paralogous loci resulting from recent gene duplications; and (3) showing that such logi provide a measure of population differentiation. Regarding the drivers of biodiversity excess within tropical mountains, I used landscape genomic analyses and ddRAD data to examine two plant species from the alpine grasslands of the Transmexican Volcanic Belt. As a main result, this thesis supports from a population-level perspective that tropical mountains; (1) allow for long-term in situ population persistence; and (2) promote population differentiation as a function of topographic isolation
Migration of Applications across Object-Oriented APIs
Software developers often encapsulate reusable code as Application Programming Interfaces (APIs). The co-evolution of applications and APIs may motivate an API migration: the replacement of application dependencies to an original API by dependencies to an alternative API that provides similar functionality and abstractions.
In this dissertation, we investigate issues associated with API migration in object-oriented systems, with special focus on wrapping approaches. We present two studies and a set of developer interviews that elicit issues in the process and techniques used in API migration in practice. The results suggest that the most pressing issues relate to discovery and specification of differences between APIs, and to assessment of migration correctness. This dissertation introduces techniques and a method to address these issues.
We propose the use of design patterns to support the specification of API wrappers. API wrapping design patterns encode solutions to common wrapping design problems. We present an initial catalog of such patterns that were abstracted from programming idioms found in existing API wrappers.
We introduce the concept of compliance testing for API migration, a form of automated testing. Compliance testing supports the discovery of behavioral differences between a wrapper and its corresponding original API, as well as assessment of wrapper correctness. Compliance testing uses API contracts and assertion tunings to explicitly capture and enforce the notion of a “good enough” wrapper that is informal in practice.
We present the Koloo method for wrapper-based API migration. The method prescribes practical steps to use compliance testing as a means to elicit the requirements for the API migration, and to assess its correctness. Koloo fits within the iterative, sample-driven general API migration process usually followed by developers in practice.
We evaluate the Koloo method in an empirical study. The subjects cover the domains of XML processing, GUI programming and bytecode engineering. The results provide evidence that Koloo is superior to alternative methods in driving the development of a wrapper that is tailored for the application under migration. The results also show that API contracts help driving the evolution of the wrapper, and assertion tuning is necessary to relax the semantics of strict equality contracts, and useful to compromise on features that are difficult to emulate perfectly. Finally, we validate that the proposed design patterns are used in practical wrappers
Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma
Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethiON platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from specific chromosomes of the long-read data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialised joint calling algorithms. We find the comparative genome-wide performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6 Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans
Genome data from a sixteenth century pig illuminate modern breed relationships
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds
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