Systems And Methods For Visualization Of Exception Handling Constructs

Disclosed are various embodiments for visualization of exception-handling constructs. In one embodiment, among others, a system includes at least one computing device; a program maintained in a memory accessible to the at least one computing device; and logic executable in the at least one computing device configured to analyze the program to determine exception-handling information; generate a graphical user interface based upon the exception-handling information; and provide the graphical user interface for display on a display device.Georgia Tech Research Corporatio

A Lightweight Visualization of Interprocedural Data-Flow Paths for Source Code Reading

Program Comprehension (ICPC), 2012 IEEE 20th International Conference onDate of Conference:11-13 June 2012Conference Location :Passa

Detecting and correcting errors in parallel object oriented systems

Our research concerns the development of an operational formalism for the in-source specification of parallel, object oriented systems. These specifications are used to enunciate the behavioural semantics of objects, as a means of enhancing their reliability. A review of object oriented languages concludes that the advance in language sophistication heralded by the object oriented paradigm has, so far, failed to produce a commensurate increase in software reliability. The lack of support in modern object oriented languages for the notion of 'valid object behaviour', as distinct from state and operations, undermines the potential power of the abstraction. Furthermore, it weakens the ability of such languages to detect behavioural problems, manifest at run-time. As a result, in-language facilities for the signalling and handling of undesirable program behaviours or states (for example, assertions) are still in their infancy. This is especially true of parallel systems, where the scope for subtle error is greater. The first goal of this work was to construct an operational model of a general purpose, parallel, object oriented system in order to ascertain the fundamental set of event classes that constitute its observable behaviour. Our model is built on the CSP process calculus and uses a subset of the Z notation to express some aspects of state. This alphabet was then used to construct a formalism designed to augment each object type description with the operational specification of an object's behaviour: Event Pattern Specifications (EPS). EPSs are a labeled list of acceptable object behaviours which form part of the definition of every type. The thesis includes a description of the design and implementation of EPSs as part of an exception handling mechanism for the parallel, object oriented language Solve. Using this implementation, we have established that the run-time checking of EPS specifications is feasible, albeit it with considerable overhead. Issues arising from this implementation are discussed and we describe the visualization of EPSs and their use in semantic browsing

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

In the Age of Web: Typed Functional-First Programming Revisited

Most programming languages were designed before the age of web. This matters because the web changes many assumptions that typed functional language designers take for granted. For example, programs do not run in a closed world, but must instead interact with (changing and likely unreliable) services and data sources, communication is often asynchronous or event-driven, and programs need to interoperate with untyped environments. In this paper, we present how the F# language and libraries face the challenges posed by the web. Technically, this comprises using type providers for integration with external information sources and for integration with untyped programming environments, using lightweight meta-programming for targeting JavaScript and computation expressions for writing asynchronous code. In this inquiry, the holistic perspective is more important than each of the features in isolation. We use a practical case study as a starting point and look at how F# language and libraries approach the challenges posed by the web. The specific lessons learned are perhaps less interesting than our attempt to uncover hidden assumptions that no longer hold in the age of web.Comment: In Proceedings ML/OCaml 2014, arXiv:1512.0143

Experiences In Migrating An Industrial Application To Aspects

Aspect-Oriented Software Development (AOSD) is a paradigm aiming to solve problems of object-oriented programming (OOP). With normal OOP it’s often unlikely to accomplish fine system modularity due to crosscutting concerns being scattered and tangled throughout the system. AOSD resolves this problem by its capability to crosscut the regular code and as a consequence transfer the crosscutting concerns to a single model called aspect. This thesis describes an experiment on industrial application wherein the effectiveness of aspect-oriented techniques is explained in migration the OOP application into aspects. The experiment goals at first to identify the crosscutting concerns in source code of the industrial application and transform these concerns to a functionally equivalent aspect-oriented version. In addition to presenting experiences gained through the experiment, the thesis aims to provide practical guidance of aspect solutions in a real application

Dynamic Analysis can be Improved with Automatic Test Suite Refactoring

Context: Developers design test suites to automatically verify that software meets its expected behaviors. Many dynamic analysis techniques are performed on the exploitation of execution traces from test cases. However, in practice, there is only one trace that results from the execution of one manually-written test case. Objective: In this paper, we propose a new technique of test suite refactoring, called B-Refactoring. The idea behind B-Refactoring is to split a test case into small test fragments, which cover a simpler part of the control flow to provide better support for dynamic analysis. Method: For a given dynamic analysis technique, our test suite refactoring approach monitors the execution of test cases and identifies small test cases without loss of the test ability. We apply B-Refactoring to assist two existing analysis tasks: automatic repair of if-statements bugs and automatic analysis of exception contracts. Results: Experimental results show that test suite refactoring can effectively simplify the execution traces of the test suite. Three real-world bugs that could previously not be fixed with the original test suite are fixed after applying B-Refactoring; meanwhile, exception contracts are better verified via applying B-Refactoring to original test suites. Conclusions: We conclude that applying B-Refactoring can effectively improve the purity of test cases. Existing dynamic analysis tasks can be enhanced by test suite refactoring

Defect Prediction using Exception Handling Method Call Structures

The main purpose of exception handling mechanisms is to improve software robustness by handling exceptions when they occur. However, empirical evidence indicates that improper implementation of exception handling code can be a source of faults in software systems. There is still limited empirical knowledge about the relationship between exception handling code and defects. In this dissertation, we present three case studies investigating defect densities of exception handling code. The results show that in every system under study, the defect density of exception handling code was significantly higher than the defect density of overall source code and normal code. The ability to predict the location of faults can assist in directing quality enhancement efforts to modules that are likely to have faults. This information can be used to guide test plans, narrow the test space, and improve software quality. We hypothesize that complicated exception handling structure is a predictive factor that is associated with defects. To the best of our knowledge, no study has addressed the relationship between the attributes of exception handling method call structures and defect occurrence, nor has prior work addressed fault prediction. We extract exception-based software metrics from the structural attributes of exception handling call graphs. To find out whether there are patterns of relationship between exception-based software metrics and fault-proneness, we propose a defect prediction model using exception handling call structures. We apply the J48 algorithm, which is the Java implementation of the C4.5 algorithm, to build exception defect prediction models. In two out of three systems under study, the results reveal that there are logical patterns of relationships between most class level exception metrics and fault-proneness. The accuracy of our prediction models is comparable to the results of defect prediction model studies in the literature. It was observed that our approach has somewhat worse predictive accuracy when a system has low average defects per class