Bioconductor: Open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have provided a strong basis for rapid development and deployment of innovative and flexible research software for scientific computation. A primary objective of this initiative is achievement of total remote reproducibility of novel algorithmic research results.

Dynamic Languages and Applications. Report on the Workshop Dyla 07 at ECOOP 2007

Following last two years’ workshop on dynamic languages at the ECOOP conference, the Dyla 2007 workshop was a successful and popular event. As its name implies, the workshop’s focus was on dynamic languages and their applications. Topics and discussions at the workshop included macro expansion mechanisms, extension of the method lookup algorithm, language interpretation, reflexivity and languages for mobile ad hoc networks. The main goal of this workshop was to bring together different dynamic language communities and favouring cross communities interaction. Dyla 2007 was organised as a full day meeting, partly devoted to presentation of submitted position papers and partly devoted to tool demonstration. All accepted papers can be downloaded from the workshop’s web site. In this report, we provide an overview of the presentations and a summary of discussions.

Risk analysis of light-frame wood construction due to multiple hazards

Light-frame wood buildings are widely built in the United States (U.S.). Natural hazards cause huge losses to light-frame wood construction. This study proposes methodologies and a framework to evaluate the performance and risk of light-frame wood construction. Performance-based engineering (PBE) aims to ensure that a building achieves the desired performance objectives when subjected to hazard loads. In this study, the collapse risk of a typical one-story light-frame wood building is determined using the Incremental Dynamic Analysis method. The collapse risks of buildings at four sites in the Eastern, Western, and Central regions of U.S. are evaluated. Various sources of uncertainties are considered in the collapse risk assessment so that the influence of uncertainties on the collapse risk of lightframe wood construction is evaluated. The collapse risks of the same building subjected to maximum considered earthquakes at different seismic zones are found to be non-uniform. In certain areas in the U.S., the snow accumulation is significant and causes huge economic losses and threatens life safety. Limited study has been performed to investigate the snow hazard when combined with a seismic hazard. A Filtered Poisson Process (FPP) model is developed in this study, overcoming the shortcomings of the typically used Bernoulli model. The FPP model is validated by comparing the simulation results to weather records obtained from the National Climatic Data Center. The FPP model is applied in the proposed framework to assess the risk of a light-frame wood building subjected to combined snow and earthquake loads. The snow accumulation has a significant influence on the seismic losses of the building. The Bernoulli snow model underestimates the seismic loss of buildings in areas with snow accumulation. An object-oriented framework is proposed in this study to performrisk assessment for lightframe wood construction. For home owners and stake holders, risks in terms of economic losses is much easier to understand than engineering parameters (e.g., inter story drift). The proposed framework is used in two applications. One is to assess the loss of the building subjected to mainshock-aftershock sequences. Aftershock and downtime costs are found to be important factors in the assessment of seismic losses. The framework is also applied to a wood building in the state of Washington to assess the loss of the building subjected to combined earthquake and snow loads. The proposed framework is proven to be an appropriate tool for risk assessment of buildings subjected to multiple hazards. Limitations and future works are also identified.

Test Blueprints - Exposing Side Effects in Execution Traces to Support Writing Unit Tests

Writing unit tests for legacy systems is a key maintenance task. When writing tests for object-oriented programs, objects need to be set up and the expected effects of executing the unit under test need to be verified. If developers lack internal knowledge of a system, the task of writing tests is non-trivial. To address this problem, we propose an approach that exposes side effects detected in example runs of the system and uses these side effects to guide the developer when writing tests. We introduce a visualization called Test Blueprint, through which we identify what the required fixture is and what assertions are needed to verify the correct behavior of a unit under test. The dynamic analysis technique that underlies our approach is based on both tracing method executions and on tracking the flow of objects at runtime. To demonstrate the usefulness of our approach we present results from two case studies.

Meta-Environment and Executable Meta-Language using Smalltalk: an Experience Report

Object-oriented modelling languages such as EMOF are often used to specify domain specific meta-models. However, these modelling languages lack the ability to describe behavior or operational semantics. Several approaches have used a subset of Java mixed with OCL as executable meta-languages. In this experience report we show how we use Smalltalk as an executable meta-language in the context of the Moose reengineering environment. We present how we implemented EMOF and its behavioral aspects. Over the last decade we validated this approach through incrementally building a meta-described reengineering environment. Such an approach bridges the gap between a code-oriented view and a meta-model driven one. It avoids the creation of yet another language and reuses the infrastructure and run-time of the underlying implementation language. It offers an uniform way of letting developers focus on their tasks while at the same time allowing them to meta-describe their domain model. The advantage of our approach is that developers use the same tools and environment they use for their regular tasks. Still the approach is not Smalltalk specific but can be applied to language offering an introspective API such as Ruby, Python, CLOS, Java and C#.

Exploiting Runtime Information in the IDE

Developers rely on the mechanisms provided by their IDE to browse and navigate a large software system. These mechanisms are usually based purely on a system's static source code. The static perspective, however, is not enough to understand an object-oriented program's behavior, in particular if implemented in a dynamic language. We propose to enhance IDEs with a program's runtime information (eg. message sends and type information) to support program comprehension through precise navigation and informative browsing. To precisely specify the type and amount of runtime data to gather about a system under development, dynamically and on demand, we adopt a technique known as partial behavioral reflection. We implemented navigation and browsing enhancements to an IDE that exploit this runtime information in a prototype called Hermion. We present preliminary validation of our experimental enhanced IDE by asking developers to assess its usefulness to understand an unfamiliar software system.

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.

A Calculus of Evolving Objects

The demands of developing modern, highly dynamic applications have led to an increasing interest in dynamic programming languages and mechanisms. Not only applications must evolve over time, but the object models themselves may need to be adapted to the requirements of different run-time contexts. Class-based models and prototype-based models, for example, may need to co-exist to meet the demands of dynamically evolving applications. Multi-dimensional dispatch, fine-grained and dynamic software composition, and run-time evolution of behaviour are further examples of diverse mechanisms which may need to co-exist in a dynamically evolving run-time environment How can we model the semantics of these highly dynamic features, yet still offer some reasonable safety guarantees? To this end we present an original calculus in which objects can adapt their behaviour at run-time to changing contexts. Both objects and environments are represented by first-class mappings between variables and values. Message sends are dynamically resolved to method calls. Variables may be dynamically bound, making it possible to model a variety of dynamic mechanisms within the same calculus. Despite the highly dynamic nature of the calculus, safety properties are assured by a type assignment system.

Augmenting Static Source Views in IDEs with Dynamic Metrics

Mainstream IDEs such as Eclipse support developers in managing software projects mainly by offering static views of the source code. Such a static perspective neglects any information about runtime behavior. However, object-oriented programs heavily rely on polymorphism and late-binding, which makes them difficult to understand just based on their static structure. Developers thus resort to debuggers or profilers to study the system's dynamics. However, the information provided by these tools is volatile and hence cannot be exploited to ease the navigation of the source space. In this paper we present an approach to augment the static source perspective with dynamic metrics such as precise runtime type information, or memory and object allocation statistics. Dynamic metrics can leverage the understanding for the behavior and structure of a system. We rely on dynamic data gathering based on aspects to analyze running Java systems. By solving concrete use cases we illustrate how dynamic metrics directly available in the IDE are useful. We also comprehensively report on the efficiency of our approach to gather dynamic metrics.

Senseo: Enriching Eclipse's Static Source Views with Dynamic Metrics

Maintaining object-oriented systems that use inheritance and polymorphism is difficult, since runtime information, such as which methods are actually invoked at a call site, is not visible in the static source code. We have implemented Senseo, an Eclipse plugin enhancing Eclipse's static source views with various dynamic metrics, such as runtime types, the number of objects created, or the amount of memory allocated in particular methods.

The construal of constructions: causal and temporal interpretations in change constructions

In this paper I first discuss some non-causal change constructions which have largely gone unnoticed in the literature, such as The butler bowed the guests in (which is said to code mild causation) and The supporters booed Newcastle off at the interval (which only codes temporal coextension between its two constitutive subevents). Since the same structure (i.e. the transitive object-oriented change construction) can be used to code a wide spectrum of causal and temporal relations, the question arises of what cognitive mechanisms may be involved in such meaning shifts. I argue that variation can be motivated on the basis of the figure/ground segregation which the conceptualiser can impose upon the integrated scene coded by the change construction. The integrated scene depicts a force-dynamic scenario but also evokes a unique temporal setting (i.e. temporal overlap or coextension between the constitutive subevents). Such a “bias” towards temporal overlap can be used by the conceptualiser to background causation and highlight temporal overlap interpretations. It is also shown that figure/ground segregation can be appealed to to account for the causal interpretation of intransitive change constructions, e.g. The kettle boiled dry. If the conceptual distance between the verbal event and the non-verbal event is (relatively) great, causality can be highlighted even in intransitive patterns.

A Texture-based land cover classification for the delineation of a shifting cultivation landscape in the Lao PDR using landscape metrics

The delineation of shifting cultivation landscapes using remote sensing in mountainous regions is challenging. On the one hand, there are difficulties related to the distinction of forest and fallow forest classes as occurring in a shifting cultivation landscape in mountainous regions. On the other hand, the dynamic nature of the shifting cultivation system poses problems to the delineation of landscapes where shifting cultivation occurs. We present a two-step approach based on an object-oriented classification of Advanced Land Observing Satellite, Advanced Visible and Near-Infrared Spectrometer (ALOS AVNIR) and Panchromatic Remote-sensing Instrument for Stereo Mapping (ALOS PRISM) data and landscape metrics. When including texture measures in the object-oriented classification, the accuracy of forest and fallow forest classes could be increased substantially. Based on such a classification, landscape metrics in the form of land cover class ratios enabled the identification of crop-fallow rotation characteristics of the shifting cultivation land use practice. By classifying and combining these landscape metrics, shifting cultivation landscapes could be delineated using a single land cover dataset.

NextServe Framework: Supporting Services Over Content-Centric Networking

The future Internet architecture aims to reformulate the way the content/service is requested to make it location-independent. Information-Centric Networking is a new network paradigm, which tries to achieve this goal by making content objects identified and requested by name instead of address. In this paper, we extend Information-Centric Networking architecture to support services in order to be requested and invoked by names. We present NextServe framework, which is a service framework with a human-readable self-explanatory naming scheme. NextServe is inspired by the object-oriented programming paradigm and is applicable with real-world scenarios.