Defining OCL expressions using templates.

OCL expressions are an essential part of UML. The current versions of OCL fail to have a meta-model which means that the integration of OCL with the UML meta-model cannot be formally defined [1]. This can result in ambiguous descriptions of systems which may compromise designs. The need to redesign the OCL has been addressed by a number of proposals submitted to the OMG. In this paper we demonstrate how a definition for OCL can be stamped out from a small number of templates. Such an approach enables a high level of reuse and an increased confidence that the definition is correct. This work forms part of the 2U consortium’s efforts for the definition of UML 2.0

A pattern based approach to defining translations between languages.

The 2U Consortium have recently submitted a proposal for the definition of the UML 2.0 infrastructure. This uses a innovative technique of rapidly “stamping out” the definition using a small number of patterns commonly found in software architecture. The contribution of this paper is to introduce the idea of reusability of mappings between languages and defining some of the reusable mapping templates. This paper also illustrates how these templates can be used to stamp out mapping between languages by stamping out a mapping between UML and Java

A pattern based approach to defining the dynamic infrastructure of UML 2.0.

The 2U Consortium has recently submitted a proposal for the definition of the UML 2.0 infrastructure. This uses an innovative technique of rapidly “stamping out” the definition using a small number of patterns commonly found in software architecture. The patterns, their instantiation, and any further language details are described using precise class diagrams and OCL, this enables the definition to be easily understood. The main focus of the 2U approach is on the static part of the definition. A further concern when modelling software, using languages such as the UML, is describing the dynamic behaviour of the system over time. The contribution of this paper is to provide a template that can be used to “stamp out” the dynamic part of the UML 2.0 infrastructure. We argue for the suitability of the dynamic template because it makes little commitment to concrete abstractions and can, therefore, be used to support a broad spectrum of behavioural languages

Unambiguous UML submission to UML 2 infrastructure RFP (ad/00-09-01).

This is a response to the UML 2.0 Request for Proposals on Infrastructure (ad/00-09-01). We propose an architecture for the definition of UML 2.0 which supports the layered and extensible definition of UML as a family of languages, and depends on the use of package extension (composition) and package template mechanisms in the metamodelling language. This submission defines that architecture and populates it with the definition of a core foundation for the definition of structural and behavioural modelling constructs for UML. Chapter 3 (“Language Architecture”) identifies all those parts of the architecture defined in any given version of this document

Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

<p>Abstract</p> <p>Background</p> <p>The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage.</p> <p>Results</p> <p>To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain.</p> <p>Conclusion</p> <p>Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.</p

Supporting systematic reviews using LDA-based document representations

BACKGROUND: Identifying relevant studies for inclusion in a systematic review (i.e. screening) is a complex, laborious and expensive task. Recently, a number of studies has shown that the use of machine learning and text mining methods to automatically identify relevant studies has the potential to drastically decrease the workload involved in the screening phase. The vast majority of these machine learning methods exploit the same underlying principle, i.e. a study is modelled as a bag-of-words (BOW). METHODS: We explore the use of topic modelling methods to derive a more informative representation of studies. We apply Latent Dirichlet allocation (LDA), an unsupervised topic modelling approach, to automatically identify topics in a collection of studies. We then represent each study as a distribution of LDA topics. Additionally, we enrich topics derived using LDA with multi-word terms identified by using an automatic term recognition (ATR) tool. For evaluation purposes, we carry out automatic identification of relevant studies using support vector machine (SVM)-based classifiers that employ both our novel topic-based representation and the BOW representation. RESULTS: Our results show that the SVM classifier is able to identify a greater number of relevant studies when using the LDA representation than the BOW representation. These observations hold for two systematic reviews of the clinical domain and three reviews of the social science domain. CONCLUSIONS: A topic-based feature representation of documents outperforms the BOW representation when applied to the task of automatic citation screening. The proposed term-enriched topics are more informative and less ambiguous to systematic reviewers. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13643-015-0117-0) contains supplementary material, which is available to authorized users

Modeling language transformations.

The emergence of software engineering model driven application environments and techniques that enable the translation of software written in one language to another . However , this possibility is not new, the compilers have long solved this need for programming languages , existing techniques are talking about source and target languages . The diverse nature of software applications requires that software engineers use ( and adapt ) a broad spectrum of languages to represent software . This paper presents an environment and an approach to quickly describe the transformations between languages using pattern transformation

Gene-Based Sequencing Identifies Lipid-Influencing Variants with Ethnicity-Specific Effects in African Americans

<div><p>Although a considerable proportion of serum lipids loci identified in European ancestry individuals (EA) replicate in African Americans (AA), interethnic differences in the distribution of serum lipids suggest that some genetic determinants differ by ethnicity. We conducted a comprehensive evaluation of five lipid candidate genes to identify variants with ethnicity-specific effects. We sequenced <i>ABCA1</i>, <i>LCAT</i>, <i>LPL</i>, <i>PON1</i>, and <i>SERPINE1</i> in 48 AA individuals with extreme serum lipid concentrations (high HDLC/low TG or low HDLC/high TG). Identified variants were genotyped in the full population-based sample of AA (n = 1694) and tested for an association with serum lipids. rs328 (<i>LPL</i>) and correlated variants were associated with higher HDLC and lower TG. Interestingly, a stronger effect was observed on a “European” vs. “African” genetic background at this locus. To investigate this effect, we evaluated the region among West Africans (WA). For TG, the effect size among WA was the same in AA with only African local ancestry (2–3% lower TG), while the larger association among AA with local European ancestry matched previous reports in EA (10%). For HDLC, there was no association with rs328 in AA with only African local ancestry or in WA, while the association among AA with European local ancestry was much greater than what has been observed for EA (15 vs. ∼5 mg/dl), suggesting an interaction with an environmental or genetic factor that differs by ethnicity. Beyond this ancestry effect, the importance of African ancestry-focused, sequence-based work was also highlighted by serum lipid associations of variants that were in higher frequency (or present only) among those of African ancestry. By beginning our study with the sequence variation present in AA individuals, investigating local ancestry effects, and seeking replication in WA, we were able to comprehensively evaluate the role of a set of candidate genes in serum lipids in AA.</p></div