Structured Review of the Evidence for Effects of Code Duplication on Software Quality

This report presents the detailed steps and results of a structured review of code clone literature. The aim of the review is to investigate the evidence for the claim that code duplication has a negative effect on code changeability. This report contains only the details of the review for which there is not enough place to include them in the companion paper published at a conference (Hordijk, Ponisio et al. 2009 - Harmfulness of Code Duplication - A Structured Review of the Evidence)

The Role of Retrotransposons in Gene Family Expansions: Insights from the Mouse \u3ci\u3eAbp\u3c/i\u3e Gene Family

Background: Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes. Results: Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome. Conclusions: We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in the most recent duplication are the main contributions of our study

Structured Review of Code Clone Literature

This report presents the results of a structured review of code clone literature. The aim of the review is to assemble a conceptual model of clone-related concepts which helps us to reason about clones. This conceptual model unifies clone concepts from a wide range of literature, so that findings about clones can be compared with each other

An Extended Stable Marriage Problem Algorithm for Clone Detection

Code cloning negatively affects industrial software and threatens intellectual property. This paper presents a novel approach to detecting cloned software by using a bijective matching technique. The proposed approach focuses on increasing the range of similarity measures and thus enhancing the precision of the detection. This is achieved by extending a well-known stable-marriage problem (SMP) and demonstrating how matches between code fragments of different files can be expressed. A prototype of the proposed approach is provided using a proper scenario, which shows a noticeable improvement in several features of clone detection such as scalability and accuracy.Comment: 20 pages, 10 figures, 6 table

Privacy-Preserving Reengineering of Model-View-Controller Application Architectures Using Linked Data

When a legacy system’s software architecture cannot be redesigned, implementing additional privacy requirements is often complex, unreliable and costly to maintain. This paper presents a privacy-by-design approach to reengineer web applications as linked data-enabled and implement access control and privacy preservation properties. The method is based on the knowledge of the application architecture, which for the Web of data is commonly designed on the basis of a model-view-controller pattern. Whereas wrapping techniques commonly used to link data of web applications duplicate the security source code, the new approach allows for the controlled disclosure of an application’s data, while preserving non-functional properties such as privacy preservation. The solution has been implemented and compared with existing linked data frameworks in terms of reliability, maintainability and complexity

Astro-WISE: Chaining to the Universe

The recent explosion of recorded digital data and its processed derivatives threatens to overwhelm researchers when analysing their experimental data or when looking up data items in archives and file systems. While current hardware developments allow to acquire, process and store 100s of terabytes of data at the cost of a modern sports car, the software systems to handle these data are lagging behind. This general problem is recognized and addressed by various scientific communities, e.g., DATAGRID/EGEE federates compute and storage power over the high-energy physical community, while the astronomical community is building an Internet geared Virtual Observatory, connecting archival data. These large projects either focus on a specific distribution aspect or aim to connect many sub-communities and have a relatively long trajectory for setting standards and a common layer. Here, we report "first light" of a very different solution to the problem initiated by a smaller astronomical IT community. It provides the abstract "scientific information layer" which integrates distributed scientific analysis with distributed processing and federated archiving and publishing. By designing new abstractions and mixing in old ones, a Science Information System with fully scalable cornerstones has been achieved, transforming data systems into knowledge systems. This break-through is facilitated by the full end-to-end linking of all dependent data items, which allows full backward chaining from the observer/researcher to the experiment. Key is the notion that information is intrinsic in nature and thus is the data acquired by a scientific experiment. The new abstraction is that software systems guide the user to that intrinsic information by forcing full backward and forward chaining in the data modelling.Comment: To be published in ADASS XVI ASP Conference Series, 2006, R. Shaw, F. Hill and D. Bell, ed