eFLINT: a domain-specific language for executable norm specifications

Software systems that share potentially sensitive data are subjected to laws, regulations, policies and/or contracts. The monitoring, control and enforcement processes applied to these systems are currently to a large extent manual, which we rather automate by embedding the processes as dedicated and adaptable software services in order to improve efficiency and effectiveness. This approach requires such regulatory services to be closely aligned with a formal description of th

Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring

Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across three to five chromosomes. Two mothers did not show any phenotypic abnormalities, although 3-13 protein-coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy-number changes in two children. This resulted in gene-dosage changes, which are probably responsible for the severe congenital phenotypes of these two children. In contrast, the third child, who has a severe congenital disease, harbored all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy-number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals affects reproduction and is expected to substantially increase the risk of miscarriages, abortions, and severe congenital disease. © 2015 The American Society of Human Genetics

<i>ICoLa</i>: A Compositional Meta-Language with Support for Incremental Language Development

Programming languages providing high-level abstractions can increase programmers’ productivity and program safety. Language-oriented programming is a paradigm in which domain-specific languages are developed to solve problems within specific domains with (high-level) abstractions relevant to those domains. However, language development involves complex design and engineering processes. These processes can be simplified by reusing (parts of) existing languages and by offering language-parametric tooling. In this paper we present iCoLa, a meta-language supporting incremental (meta-)programming based on reusable components. In our implementation of iCoLa, languages are first-class citizens, providing the full power of the host-language (Haskell) to compose and manipulate languages. We demonstrate iCoLa through the construction of the Imp, SIMPLE, and MiniJava languages via the composition and restriction of language fragments and demonstrate the variability of our approach through the construction of several languages using a fixed-set of operators.</p

Making the Invisible Visible in Computational Notebooks

Notebooks are increasingly popular programming tools adopted by a diverse range of users, including professional and novice users, from various fields not necessarily skilled in software engineering, to experiment with programming and develop software. Notebooks are often used within interactive and exploratory programming settings; however, some of their main use cases are not naturally supported by their design. For example, users can only get insights into the program’s state by executing program fragments and updating one’s mental model. This paper discusses the possibility of defining widgets to improve notebooks by providing direct insights into the program state. The widgets are developed upon previous work in which a novel approach to incremental programming is suggested based on the notion of an exploring interpreter. As example, we present widgets for visualizing execution history and variable assignments, thereby reducing the cognitive load on users