Reusability in software engineering

This paper surveys recent work concerning reusability in software engineering. The current directions in software reusability are discussed, and the two major approaches of reusable building blocks and reusable patterns studied. An extensive bibliography, parts of which are annotated, is included

Support for collaborative component-based software engineering

Collaborative system composition during design has been poorly supported by traditional CASE tools (which have usually concentrated on supporting individual projects) and almost exclusively focused on static composition. Little support for maintaining large distributed collections of heterogeneous software components across a number of projects has been developed. The CoDEEDS project addresses the collaborative determination, elaboration, and evolution of design spaces that describe both static and dynamic compositions of software components from sources such as component libraries, software service directories, and reuse repositories. The GENESIS project has focussed, in the development of OSCAR, on the creation and maintenance of large software artefact repositories. The most recent extensions are explicitly addressing the provision of cross-project global views of large software collections and historical views of individual artefacts within a collection. The long-term benefits of such support can only be realised if OSCAR and CoDEEDS are widely adopted and steps to facilitate this are described. This book continues to provide a forum, which a recent book, Software Evolution with UML and XML, started, where expert insights are presented on the subject. In that book, initial efforts were made to link together three current phenomena: software evolution, UML, and XML. In this book, focus will be on the practical side of linking them, that is, how UML and XML and their related methods/tools can assist software evolution in practice. Considering that nowadays software starts evolving before it is delivered, an apparent feature for software evolution is that it happens over all stages and over all aspects. Therefore, all possible techniques should be explored. This book explores techniques based on UML/XML and a combination of them with other techniques (i.e., over all techniques from theory to tools). Software evolution happens at all stages. Chapters in this book describe that software evolution issues present at stages of software architecturing, modeling/specifying, assessing, coding, validating, design recovering, program understanding, and reusing. Software evolution happens in all aspects. Chapters in this book illustrate that software evolution issues are involved in Web application, embedded system, software repository, component-based development, object model, development environment, software metrics, UML use case diagram, system model, Legacy system, safety critical system, user interface, software reuse, evolution management, and variability modeling. Software evolution needs to be facilitated with all possible techniques. Chapters in this book demonstrate techniques, such as formal methods, program transformation, empirical study, tool development, standardisation, visualisation, to control system changes to meet organisational and business objectives in a cost-effective way. On the journey of the grand challenge posed by software evolution, the journey that we have to make, the contributory authors of this book have already made further advances

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

Prototyping the recursive internet architecture: the IRATI project approach

In recent years, many new Internet architectures are being proposed to solve shortcomings in the current Internet. A lot of these new architectures merely extend the current TCP/IP architecture and hence do not solve the fundamental cause of these problems. The Recursive Internet Architecture (RINA) is a true new network architecture, developed from scratch, building on lessons learned in the past. RINA prototyping efforts have been ongoing since 2010, but a prototype on which a commercial RINA implementation can be built has not been developed yet. The goal of the IRATI research project is to develop and evaluate such a prototype in Linux/OS. This article focuses on the software design required to implement a network stack in Linux/OS. We motivate the placement of, and communication between, the different software components in either the kernel or user space. The first open source prototype of the IRATI implementation of RINA will be available in June 2014 for researchers, developers, and early adopters

The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus

BACKGROUND: Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic in its new host than in its native one, and is thought to threaten the endangered An. anguilla across its range. The molecular bases for the increased pathogenicity of the nematodes in their new hosts is not known. RESULTS: A reference transcriptome was assembled for A. crassus from Roche 454 pyrosequencing data. Raw reads (756,363 total) from nematodes from An. japonica and An. anguilla hosts were filtered for likely host contaminants and ribosomal RNAs. The remaining 353,055 reads were assembled into 11,372 contigs of a high confidence assembly (spanning 6.6 Mb) and an additional 21,153 singletons and contigs of a lower confidence assembly (spanning an additional 6.2 Mb). Roughly 55% of the high confidence assembly contigs were annotated with domain- or protein sequence similarity derived functional information. Sequences conserved only in nematodes, or unique to A. crassus were more likely to have secretory signal peptides. Thousands of high quality single nucleotide polymorphisms were identified, and coding polymorphism was correlated with differential expression between individual nematodes. Transcripts identified as being under positive selection were enriched in peptidases. Enzymes involved in energy metabolism were enriched in the set of genes differentially expressed between European and Asian A. crassus. CONCLUSIONS: The reference transcriptome of A. crassus is of high quality, and will serve as a basis for future work on the invasion biology of this important parasite. The polymorphisms identified will provide a key tool set for analysis of population structure and identification of genes likely to be involved in increased pathogenicity in European eel hosts. The identification of peptidases under positive selection is a first step in this programme

Open Programming Language Interpreters

Context: This paper presents the concept of open programming language interpreters and the implementation of a framework-level metaobject protocol (MOP) to support them. Inquiry: We address the problem of dynamic interpreter adaptation to tailor the interpreter's behavior on the task to be solved and to introduce new features to fulfill unforeseen requirements. Many languages provide a MOP that to some degree supports reflection. However, MOPs are typically language-specific, their reflective functionality is often restricted, and the adaptation and application logic are often mixed which hardens the understanding and maintenance of the source code. Our system overcomes these limitations. Approach: We designed and implemented a system to support open programming language interpreters. The prototype implementation is integrated in the Neverlang framework. The system exposes the structure, behavior and the runtime state of any Neverlang-based interpreter with the ability to modify it. Knowledge: Our system provides a complete control over interpreter's structure, behavior and its runtime state. The approach is applicable to every Neverlang-based interpreter. Adaptation code can potentially be reused across different language implementations. Grounding: Having a prototype implementation we focused on feasibility evaluation. The paper shows that our approach well addresses problems commonly found in the research literature. We have a demonstrative video and examples that illustrate our approach on dynamic software adaptation, aspect-oriented programming, debugging and context-aware interpreters. Importance: To our knowledge, our paper presents the first reflective approach targeting a general framework for language development. Our system provides full reflective support for free to any Neverlang-based interpreter. We are not aware of any prior application of open implementations to programming language interpreters in the sense defined in this paper. Rather than substituting other approaches, we believe our system can be used as a complementary technique in situations where other approaches present serious limitations

De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato

Background: St. John's wort (Hypericum perforatum L.) is a medicinal plant that produces important metabolites with antidepressant and anticancer activities. Recently gained biological information has shown that this species is also an attractive model system for the study of a naturally occurring form of asexual reproduction called apomixis, which allows cloning plants through seeds. In aposporic gametogenesis, one or multiple somatic cells belonging to the ovule nucellus change their fate by dividing mitotically and developing functionally unreduced embryo sacs by mimicking sexual gametogenesis. Although the introduction of apomixis into agronomically important crops could have revolutionary implications for plant breeding, the genetic control of this mechanism of seed formation is still not well understood for most of the model species investigated so far. We used Roche 454 technology to sequence the entire H. perforatum flower transcriptome of whole flower buds and single flower verticils collected from obligately sexual and unrelated highly or facultatively apomictic genotypes, which enabled us to identify RNAs that are likely exclusive to flower organs (i.e., sepals, petals, stamens and carpels) or reproductive strategies (i.e., sexual vs. apomictic). Results: Here we sequenced and annotated the flower transcriptome of H. perforatum with particular reference to reproductive organs and processes. In particular, in our study we characterized approximately 37,000 transcripts found expressed in male and/or female reproductive organs, including tissues or cells of sexual and apomictic flower buds. Ontological annotation was applied to identify major biological processes and molecular functions involved in flower development and plant reproduction. Starting from this dataset, we were able to recover and annotate a large number of transcripts related to meiosis, gametophyte/gamete formation, and embryogenesis, as well as genes that are exclusively or preferentially expressed in sexual or apomictic libraries. Real-Time RT-qPCR assays on pistils and anthers collected at different developmental stages from accessions showing alternative modes of reproduction were used to identify potential genes that are related to plant reproduction sensu lato in H. perforatum. Conclusions: Our approach of sequencing flowers from two fully obligate sexual genotypes and two unrelated highly apomictic genotypes, in addition to different flower parts dissected from a facultatively apomictic accession, enabled us to analyze the complexity of the flower transcriptome according to its main reproductive organs as well as for alternative reproductive behaviors. Both annotation and expression data provided original results supporting the hypothesis that apomixis in H. perforatum relies upon spatial or temporal mis-expression of genes acting during female sexual reproduction. The present analyses aim to pave the way toward a better understanding of the molecular basis of flower development and plant reproduction, by identifying genes or RNAs that may differentiate or regulate the sexual and apomictic reproductive pathways in H. perforatum