How Lisp systems look different

Many reverse engineering approaches have been developed to analyze software systems written in different languages like C/C++ or Java. These approaches typically rely on a meta-model, that is either specific for the language at hand or language independent (e.g. UML). However, one language that was hardly addressed is Lisp. While at first sight it can be accommodated by current language independent meta-models, Lisp has some unique features (e.g. macros, CLOS entities) that are crucial for reverse engineering Lisp systems. In this paper we propose a suite of new visualizations that reveal the special traits of the Lisp language and thus help in understanding complex Lisp systems. To validate our approach we apply them on several large Lisp case studies, and summarize our experience in terms of a series of recurring visual patterns that we have detected.

Enabling the evolution of J2EE applications through reverse engineering and quality assurance

Enterprise Applications are complex software systems that manipulate much persistent data and interact with the user through a vast and complex user interface. In particular applications written for the Java 2 Platform, Enterprise Edition (J2EE) are composed using various technologies such as Enterprise Java Beans (EJB) or Java Server Pages (JSP) that in turn rely on languages other than Java, such as XML or SQL. In this heterogeneous context applying existing reverse engineering and quality assurance techniques developed for object-oriented systems is not enough. Because those techniques have been created to measure quality or provide information about one aspect of J2EE applications, they cannot properly measure the quality of the entire system. We intend to devise techniques and metrics to measure quality in J2EE applications considering all their aspects and to aid their evolution. Using software visualization we also intend to inspect to structure of J2EE applications and all other aspects that can be investigate through this technique. In order to do that we also need to create a unified meta-model including all elements composing a J2EE application.

Computational fluid dynamics modelling in cardiovascular medicine.

This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges.

Lessons in Software Evolution Learned by Listening to Smalltalk

The biggest challenge facing software developers today is how to gracefully evolve complex software systems in the face of changing requirements. We clearly need software systems to be more dynamic, compositional and model-centric, but instead we continue to build systems that are static, baroque and inflexible. How can we better build change-enabled systems in the future? To answer this question, we propose to look back to one of the most successful systems to support change, namely Smalltalk. We briefly introduce Smalltalk with a few simple examples, and draw some lessons for software evolution. Smalltalk's simplicity, its reflective design, and its highly dynamic nature all go a long way towards enabling change in Smalltalk applications. We then illustrate how these lessons work in practice by reviewing a number of research projects that support software evolution by exploiting Smalltalk's design. We conclude by summarizing open issues and challenges for change-enabled systems of the future.

Evaluating Code Duplication to Identify Rich Business Objects from Data Transfer Objects

Java Enterprise Applications (JEAs) are complex software systems written using multiple technologies. Moreover they are usually distributed systems and use a database to deal with persistence. A particular problem that appears in the design of these systems is the lack of a rich business model. In this paper we propose a technique to support the recovery of such rich business objects starting from anemic Data Transfer Objects (DTOs). Exposing the code duplications in the application's elements using the DTOs we suggest which business logic can be moved into the DTOs from the other classes.

Patterns of positive selection in seven ant genomes

The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide datasets in bees and flies with the same methodology, to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants.

Comparison of three optical tracking systems in a complex navigation scenario

Three-dimensional rotational X-ray imaging with the SIREMOBIL Iso-C3D (Siemens AG, Medical Solutions, Erlangen, Germany) has become a well-established intra-operative imaging modality. In combination with a tracking system, the Iso-C3D provides inherently registered image volumes ready for direct navigation. This is achieved by means of a pre-calibration procedure. The aim of this study was to investigate the influence of the tracking system used on the overall navigation accuracy of direct Iso-C3D navigation. Three models of tracking system were used in the study: Two Optotrak 3020s, a Polaris P4 and a Polaris Spectra system, with both Polaris systems being in the passive operation mode. The evaluation was carried out at two different sites using two Iso-C3D devices. To measure the navigation accuracy, a number of phantom experiments were conducted using an acrylic phantom equipped with titanium spheres. After scanning, a special pointer was used to pinpoint these markers. The difference between the digitized and navigated positions served as the accuracy measure. Up to 20 phantom scans were performed for each tracking system. The average accuracy measured was 0.86 mm and 0.96 mm for the two Optotrak 3020 systems, 1.15 mm for the Polaris P4, and 1.04 mm for the Polaris Spectra system. For the Polaris systems a higher maximal error was found, but all three systems yielded similar minimal errors. On average, all tracking systems used in this study could deliver similar navigation accuracy. The passive Polaris system showed ? as expected ? higher maximal errors; however, depending on the application constraints, this might be negligible.

A global ”imaging” view on systems approaches in immunology

The immune system exhibits an enormous complexity. High throughput methods such as the "-omic'' technologies generate vast amounts of data that facilitate dissection of immunological processes at ever finer resolution. Using high-resolution data-driven systems analysis, causal relationships between complex molecular processes and particular immunological phenotypes can be constructed. However, processes in tissues, organs, and the organism itself (so-called higher level processes) also control and regulate the molecular (lower level) processes. Reverse systems engineering approaches, which focus on the examination of the structure, dynamics and control of the immune system, can help to understand the construction principles of the immune system. Such integrative mechanistic models can properly describe, explain, and predict the behavior of the immune system in health and disease by combining both higher and lower level processes. Moving from molecular and cellular levels to a multiscale systems understanding requires the development of methodologies that integrate data from different biological levels into multiscale mechanistic models. In particular, 3D imaging techniques and 4D modeling of the spatiotemporal dynamics of immune processes within lymphoid tissues are central for such integrative approaches. Both dynamic and global organ imaging technologies will be instrumental in facilitating comprehensive multiscale systems immunology analyses as discussed in this review.

Software Engineering for Self-Adaptive Systems: A Second Research Roadmap

The goal of this roadmap paper is to summarize the state-of-the-art and identify research challenges when developing, deploying and managing self-adaptive software systems. Instead of dealing with a wide range of topics associated with the field, we focus on four essential topics of self-adaptation: design space for self-adaptive solutions, software engineering processes for self-adaptive systems, from centralized to decentralized control, and practical run-time verification & validation for self-adaptive systems. For each topic, we present an overview, suggest future directions, and focus on selected challenges. This paper complements and extends a previous roadmap on software engineering for self-adaptive systems published in 2009 covering a different set of topics, and reflecting in part on the previous paper. This roadmap is one of the many results of the Dagstuhl Seminar 10431 on Software Engineering for Self-Adaptive Systems, which took place in October 2010.

Impact of dams, dam removal and dam-related river engineering structures on sediment connectivity and channel morphology of the Fugnitz and the Kaja Rivers

In terms of changing flow and sediment regimes of rivers, dams are often regarded as the most dominant form of human impact on fluvial systems. Dams can decrease the flux of water and sediments leading to channel changes such as upstream aggradation and downstream degradation. The opposite effects occur when dams are removed. Channel degradation often requires further intervention in terms of river bed and bank protection works. The situation evolves more complex in river systems that are impacted by a series of dams due to feedback processes between the different system compartments. A number of studies have recently investigated geomorphic systems using connectivity approaches to improve the understanding of geomorphic system response to change. This paper presents a case study investigating the impact of dam construction, dam removal and dam-related river bed and bank protection measures on the sediment connectivity and channel morphology of the Fugnitz and the Kaja Rivers using a combination of DEM analyses, field surveys and landscape evolution modelling. For both river systems the results revealed low sediment connectivity accompanied by a fine river bed sediment facies in river sections upstream of active dams and of removed dams with protection measures. Contrarily, high sediment connectivity which was accompanied by a coarse river bed sediment facies was observed in river sections either located downstream of active dams or of removed dams with upstream protection. In terms of channel changes, significant channel degradation was examined at locations downstream of active dams and of removed dams. Channel bed and bank protection measures prevent erosion and channel slope recovery after dam removal. Landscape evolution modeling revealed a complex geomorphic response to dam construction and dam removal as sediment output rates and therefore geomorphic processes have been shown to act in a non-linear manner. These insights are deemed to have major implications for river management and conservation, as quality and state of riverine habitats are determined by channel morphology and river bed sediment composition.