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

A framework to maximise the communicative power of knowledge visualisations

Knowledge visualisation, in the field of information systems, is both a process and a product, informed by the closely aligned fields of information visualisation and knowledg management. Knowledge visualisation has untapped potential within the purview of knowledge communication. Even so, knowledge visualisations are infrequently deployed due to a lack of evidence-based guidance. To improve this situation, we carried out a systematic literature review to derive a number of “lenses” that can be used to reveal the essential perspectives to feed into the visualisation production process.We propose a conceptual framework which incorporates these lenses to guide producers of knowledge visualisations. This framework uses the different lenses to reveal critical perspectives that need to be considered during the design process. We conclude by demonstrating how this framework could be used to produce an effective knowledge visualisation

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

i-JEN: Visual interactive Malaysia crime news retrieval system

Supporting crime news investigation involves a mechanism to help monitor the current and past status of criminal events. We believe this could be well facilitated by focusing on the user interfaces and the event crime model aspects. In this paper we discuss on a development of Visual Interactive Malaysia Crime News Retrieval System (i-JEN) and describe the approach, user studies and planned, the system architecture and future plan. Our main objectives are to construct crime-based event; investigate the use of crime-based event in improving the classification and clustering; develop an interactive crime news retrieval system; visualize crime news in an effective and interactive way; integrate them into a usable and robust system and evaluate the usability and system performance. The system will serve as a news monitoring system which aims to automatically organize, retrieve and present the crime news in such a way as to support an effective monitoring, searching, and browsing for the target users groups of general public, news analysts and policemen or crime investigators. The study will contribute to the better understanding of the crime data consumption in the Malaysian context as well as the developed system with the visualisation features to address crime data and the eventual goal of combating the crimes

Agent-based simulation of open source evolution

We present an agent-based simulation model developed to study how size, complexity and effort relate to each other in the development of open source software (OSS). In the model, many developer agents generate, extend, and re-factor code modules independently and in parallel. This accords with empirical observations of OSS development. To our knowledge, this is the first model of OSS evolution that includes the complexity of software modules as a limiting factor in productivity, the fitness of the software to its requirements, and the motivation of developers. Validation of the model was done by comparing the simulated results against four measures of software evolution (system size, proportion of highly complex modules, level of complexity control work, and distribution of changes) for four large OSS systems. The simulated results resembled the observed data, except for system size: three of the OSS systems showed alternating patterns of super-linear and sub-linear growth, while the simulations produced only super-linear growth. However, the fidelity of the model for the other measures suggests that developer motivation and the limiting effect of complexity on productivity have a significant effect on the development of OSS systems and should be considered in any model of OSS development

Introductory programming: a systematic literature review

As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming. This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research