Sara Kalvala

Spatial simulations of myxobacterial development

Many bacteria exhibit multicellular behaviour, with individuals within a colony coordinating their actions for communal benefit. One example of complex multicellular phenotypes is myxobacterial fruiting body formation, where thousands of cells aggregate into large three-dimensional structures, within which sporulation occurs. Here we describe a novel theoretical model, which uses Monte Carlo dynamics to simulate and explain multicellular development. The model captures multiple behaviours observed during fruiting, including the spontaneous formation of aggregation centres and the formation and dissolution of fruiting bodies. We show that a small number of physical properties in the model is sufficient to explain the most frequently documented population-level behaviours observed during development in Myxococcus xanthus.

Program transformations using temporal logic side conditions

This article describes an approach to program optimization based on transformations, where temporal logic is used to specify side conditions, and strategies are created which expand the repertoire of transformations and provide a suitable level of abstraction. We demonstrate the power of this approach by developing a set of optimizations using our transformation language and showing how the transformations can be converted into a form which makes it easier to apply them, while maintaining trust in the resulting optimizing steps. The approach is illustrated through a transformational case study where we apply several optimizations to a small program.

Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates

Synthetic Biology aspires to design, compose and engineer biological systems that implement specified behaviour. When designing such systems, hypothesis testing via computational modelling and simulation is vital in order to reduce the need of costly wet lab experiments. As a case study, we discuss the use of computational modelling and stochastic simulation for engineered genetic circuits that implement Boolean AND and OR gates that have been reported in the literature. We present performance analysis results for nine different state-of-the-art stochastic simulation algorithms and analyse the dynamic behaviour of the proposed gates. Stochastic simulations verify the desired functioning of the proposed gate designs.

Understanding initial undergraduate expectations and identity in computing studies

ABSTRACT There is growing appreciation of the importance of understanding the student perspective in Higher Education (HE) at both institutional and international levels. This is particularly important in Science, Technology, Engineering and Mathematics subjects such as Computer Science (CS) and Engineering in which industry needs are high but so are student dropout rates. An important factor to consider is the management of students’ initial expectations of university study and career. This paper reports on a study of CS first-year students’ expectations across three European countries using qualitative data from student surveys and essays. Expectation is examined from both short-term (topics to be studied) and long-term (career goals) perspectives. Tackling these issues will help paint a picture of computing education through students’ eyes and explore their vision of its and their role in society. It will also help educators prepare students more effectively for university study and to improve the student experience.

Race conditions in message sequence charts

Message Sequence Charts (MSCs) are a graphical language for the description of scenarios in terms of message exchanges between communicating components in a distributed environment. The language has been standardised by the ITU and given a formal semantics by means of a process algebra. In this paper, we review a design anomaly, called race condition, in an MSC specification and argue that the current solution correcting race conditions is too weak when implementation is considered. In this paper, we provide an algorithm on partial orders as our solution. The result is a strengthened partial order, which is race-free and remains race-free in the implementation.

A process-based semantics for message sequence charts with data

Message sequence charts (MSCs) are a graphical language for scenarios of communicating components exchanging messages in a distributed environment. The language has been standardised by the International Telecommunication Union (ITU) and given a formal semantics by means of process algebra. Nevertheless, little attention has been given to MSCs where a message with data is a building block. In this paper, we investigate the impact that the concept of data flow brings to the conventional semantics, and propose a CCS-like process calculus as an alternative formal framework. The proposed semantics captures the data flow properties while maintaining the expressiveness of the conventional semantics. Equivalence of MSCs is also discussed from the perspective of the corresponding process equivalence.

Engagement Measures in Massive Open Online Courses

Massive Open Online Course (MOOC) provision has proliferated over the past four years and millions of learners have participated. However, it is widely acknowledged that the number of completions is disturbingly low and MOOC drop-out rates have been a prominent issue of discussion. Currently, most MOOC analysis focuses on aspects such as patterns of engagement and prediction of dropout using data obtained by applying learning analytics to the large amounts of data gathered. In contrast, the effectiveness of teaching and learning programs in traditional face-to-face Higher Education (HE) settings is increasingly being assessed by measures linked to the promotion of student engagement. Internationally, student engagement surveys are being used to provide profiles of the effectiveness of teaching and learning within and between courses. In this paper we consider MOOC participation and drop-out issues emerging from the literature, and provide an overview of the student engagement surveys now widely used in HE. MOOC pedagogy is examined from the perspective of student engagement and we identify the need for a similar model adapted to MOOCs which could provide both a framework for course development and an instrument to assess aspects of teaching and learning in existing courses.

From Specification to Optimisation: An Architecture for Optimisation of Java Bytecode

We present the architecture of the Rosser toolkit that allows optimisations to be specified in a domain specific language, then compiled and deployed towards optimising object programs. The optimisers generated by Rosser exploit model checking to apply dataflow analysis to programs to find optimising opportunities. The transformational language is derived from a formal basis and consequently can be proved sound. We validate the technique by comparing the application of optimisers generated by our system against hand-written optimisations using the Java based Scimark 2.0 benchmark.

Student engagement in massive open online courses

Completion rates in massive open online courses MOOCs are disturbingly low. Existing analysis has focused on patterns of resource access and prediction of drop-out using learning analytics. In contrast, the effectiveness of teaching programs in traditional higher education HE settings internationally is increasingly assessed by surveys measuring student engagement. The conceptualisation of engagement used is much richer and more informative than the way the term is currently interpreted in the context of MOOCs. This paper considers MOOC participation, learning and drop-out in the context of this richer conceptualisation of student engagement. MOOC pedagogy and practice are examined and we evaluate how far HE engagement measures can be successfully used in the MOOC context. We identify the need for a MOOC engagement model and suggest recommendations for basic, initial steps which MOOC developers can make towards improving engagement.

A formal approach to fixing bugs

Bugs within programs typically arise within well-known motifs, such as complex language features or misunderstood programming interfaces. Some software development tools often detect some of these situations, and some integrated development environments suggest automated fixes for some of the simple cases. However, it is usually difficult to hand-craft and integrate more complex bug-fixing into these environments. We present a language for specifying program transformations which is paired with a novel methodology for identifying and fixing bug patterns within Java source code. We propose a combination of source code and bytecode analyses: this allows for using the control flow in the bytecode to help identify the bugs while generating corrected source code. The specification language uses a combination of syntactic rewrite rules and dataflow analysis generated from temporal logic based conditions. We demonstrate the approach with a prototype implementation.