Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

Animating the evolution of software

The use and development of open source software has increased significantly in the last decade. The high frequency of changes and releases across a distributed environment requires good project management tools in order to control the process adequately. However, even with these tools in place, the nature of the development and the fact that developers will often work on many other projects simultaneously, means that the developers are unlikely to have a clear picture of the current state of the project at any time. Furthermore, the poor documentation associated with many projects has a detrimental effect when encouraging new developers to contribute to the software. A typical version control repository contains a mine of information that is not always obvious and not easy to comprehend in its raw form. However, presenting this historical data in a suitable format by using software visualisation techniques allows the evolution of the software over a number of releases to be shown. This allows the changes that have been made to the software to be identified clearly, thus ensuring that the effect of those changes will also be emphasised. This then enables both managers and developers to gain a more detailed view of the current state of the project. The visualisation of evolving software introduces a number of new issues. This thesis investigates some of these issues in detail, and recommends a number of solutions in order to alleviate the problems that may otherwise arise. The solutions are then demonstrated in the definition of two new visualisations. These use historical data contained within version control repositories to show the evolution of the software at a number of levels of granularity. Additionally, animation is used as an integral part of both visualisations - not only to show the evolution by representing the progression of time, but also to highlight the changes that have occurred. Previously, the use of animation within software visualisation has been primarily restricted to small-scale, hand generated visualisations. However, this thesis shows the viability of using animation within software visualisation with automated visualisations on a large scale. In addition, evaluation of the visualisations has shown that they are suitable for showing the changes that have occurred in the software over a period of time, and subsequently how the software has evolved. These visualisations are therefore suitable for use by developers and managers involved with open source software. In addition, they also provide a basis for future research in evolutionary visualisations, software evolution and open source development

Exploiting Abstract Syntax Trees to Locate Software Defects

Context. Software defect prediction aims to reduce the large costs involved with faults in a software system. A wide range of traditional software metrics have been evaluated as potential defect indicators. These traditional metrics are derived from the source code or from the software development process. Studies have shown that no metric clearly out performs another and identifying defect-prone code using traditional metrics has reached a performance ceiling. Less traditional metrics have been studied, with these metrics being derived from the natural language of the source code. These newer, less traditional and finer grained metrics have shown promise within defect prediction. Aims. The aim of this dissertation is to study the relationship between short Java constructs and the faultiness of source code. To study this relationship this dissertation introduces the concept of a Java sequence and Java code snippet. Sequences are created by using the Java abstract syntax tree. The ordering of the nodes within the abstract syntax tree creates the sequences, while small sub sequences of this sequence are the code snippets. The dissertation tries to find a relationship between the code snippets and faulty and non-faulty code. This dissertation also looks at the evolution of the code snippets as a system matures, to discover whether code snippets significantly associated with faulty code change over time. Methods. To achieve the aims of the dissertation, two main techniques have been developed; finding defective code and extracting Java sequences and code snippets. Finding defective code has been split into two areas - finding the defect fix and defect insertion points. To find the defect fix points an implementation of the bug-linking algorithm has been developed, called S + e . Two algorithms were developed to extract the sequences and the code snippets. The code snippets are analysed using the binomial test to find which ones are significantly associated with faulty and non-faulty code. These techniques have been performed on five different Java datasets; ArgoUML, AspectJ and three releases of Eclipse.JDT.core Results. There are significant associations between some code snippets and faulty code. Frequently occurring fault-prone code snippets include those associated with identifiers, method calls and variables. There are some code snippets significantly associated with faults that are always in faulty code. There are 201 code snippets that are snippets significantly associated with faults across all five of the systems. The technique is unable to find any significant associations between code snippets and non-faulty code. The relationship between code snippets and faults seems to change as the system evolves with more snippets becoming fault-prone as Eclipse.JDT.core evolved over the three releases analysed. Conclusions. This dissertation has introduced the concept of code snippets into software engineering and defect prediction. The use of code snippets offers a promising approach to identifying potentially defective code. Unlike previous approaches, code snippets are based on a comprehensive analysis of low level code features and potentially allow the full set of code defects to be identified. Initial research into the relationship between code snippets and faults has shown that some code constructs or features are significantly related to software faults. The significant associations between code snippets and faults has provided additional empirical evidence to some already researched bad constructs within defect prediction. The code snippets have shown that some constructs significantly associated with faults are located in all five systems, and although this set is small finding any defect indicators that transfer successfully from one system to another is rare

Management Aspects of Software Clone Detection and Analysis

Copying a code fragment and reusing it by pasting with or without minor modifications is a common practice in software development for improved productivity. As a result, software systems often have similar segments of code, called software clones or code clones. Due to many reasons, unintentional clones may also appear in the source code without awareness of the developer. Studies report that significant fractions (5% to 50%) of the code in typical software systems are cloned. Although code cloning may increase initial productivity, it may cause fault propagation, inflate the code base and increase maintenance overhead. Thus, it is believed that code clones should be identified and carefully managed. This Ph.D. thesis contributes in clone management with techniques realized into tools and large-scale in-depth analyses of clones to inform clone management in devising effective techniques and strategies. To support proactive clone management, we have developed a clone detector as a plug-in to the Eclipse IDE. For clone detection, we used a hybrid approach that combines the strength of both parser-based and text-based techniques. To capture clones that are similar but not exact duplicates, we adopted a novel approach that applies a suffix-tree-based k-difference hybrid algorithm, borrowed from the area of computational biology. Instead of targeting all clones from the entire code base, our tool aids clone-aware development by allowing focused search for clones of any code fragment of the developer's interest. A good understanding on the code cloning phenomenon is a prerequisite to devise efficient clone management strategies. The second phase of the thesis includes large-scale empirical studies on the characteristics (e.g., proportion, types of similarity, change patterns) of code clones in evolving software systems. Applying statistical techniques, we also made fairly accurate forecast on the proportion of code clones in the future versions of software projects. The outcome of these studies expose useful insights into the characteristics of evolving clones and their management implications. Upon identification of the code clones, their management often necessitates careful refactoring, which is dealt with at the third phase of the thesis. Given a large number of clones, it is difficult to optimally decide what to refactor and what not, especially when there are dependencies among clones and the objective remains the minimization of refactoring efforts and risks while maximizing benefits. In this regard, we developed a novel clone refactoring scheduler that applies a constraint programming approach. We also introduced a novel effort model for the estimation of efforts needed to refactor clones in source code. We evaluated our clone detector, scheduler and effort model through comparative empirical studies and user studies. Finally, based on our experience and in-depth analysis of the present state of the art, we expose avenues for further research and development towards a versatile clone management system that we envision

Using Static Analysis and Static Measurement for Industrial Software Quality Evaluation

Business organizations that outsource software development need to evaluate the quality of the code delivered by suppliers. In this paper, we illustrate an experience in setting up and using a toolset for evaluating code quality for a company that outsources software development. The selected tools perform static code analysis and static measurement, and provide evidence of possible quality issues. To verify whether the issues reported by tools are associated to real problems, code inspections were carried out. The combination of automated analysis and inspections proved effective, in that several types of defects were identified. Based on our findings, the business company was able to learn what are the most frequent and dangerous types of defects that affect the acquired code: this knowledge is now being used on a regular basis to perform focused verification activities