Aidan Delaney

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1842 taxa, 22 618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.

Evaluating and generalizing constraint diagrams

The constraint diagram language was designed to be used in conjunction with the unified modelling language (UML), primarily for placing formal constraints on software models. In particular, constraint diagrams play a similar role to the textual object constraint language (OCL) in that they can be used for specifying system invariants and operation contracts in the context of a UML model. Unlike the OCL, however, constraint diagrams can be used independently of the UML. In this paper, we illustrate a range of intuitive and counter-intuitive features of constraint diagrams and highlight some (potential) expressiveness limitations. The counter-intuitive features are related to how the individual pieces of syntax interact. A generalized version of the constraint diagram language that overcomes the illustrated counter-intuitive features and limitations is proposed. In order to discourage specification readers and writers from overlooking certain semantic information, the generalized notation allows this information to be expressed more explicitly than in the non-generalized case. The design of the generalized notation takes into account five language design principles which are discussed in the paper. We provide a formalization of the syntax and semantics for generalized constraint diagrams. Moreover, we establish a lower bound on the expressiveness of the generalized notation and show that they are at least as expressive as constraint diagrams.

SketchSet: Creating Euler diagrams using pen or mouse

Euler diagrams form the basis of various visual languages but tool support for creating them is generally limited to generic diagram editing software using mouse and keyboard interaction. A more natural and convenient mode of entry is via a sketching interface which facilitates greater cognitive focus on the task of diagram creation. Previous work has developed sketching interfaces for Euler diagrams drawn with ellipses. This paper presents SketchSet, the first sketch tool for Euler diagrams whose curves can be circles, ellipses, or arbitrary shapes. SketchSet allows the creation of formal diagrams via point and click interaction. The user drawn diagram, in sketched or formal format, is automatically converted to a diagram in the other format, thus maintaining both views. We provide a mechanism that allows semantic differences between the sketch and the formal diagram to be rectified automatically. Finally, we present a user study that evaluates the effectiveness of the tool.

Towards Overcoming Deficiencies in Constraint Diagrams

The constraint diagram language was designed to be used in conjunction with the Unified Modelling Language (UML), primarily for placing formal constraints on software models. In particular, constraint diagrams play a similar role to the textual object constraint language in that they can be used for specifying system invariants and operation contracts in the context of a UML model. Constraint diagrams can also be used independently of the UML. In this paper, we illustrate a range of counter-intuitive features of constraint diagrams and highlight some (potential) expressiveness limitations. We propose a generalized version of the constraint diagram language that overcomes the illustrated counter-intuitive features and limitations.

Spider Diagrams of Order and a Hierarchy of Star-Free Regular Languages

The spider diagram logic forms a fragment of the constraint diagram logic and was designed to be primarily used as a diagrammatic software specification tool. Our interest is in using the logical basis of spider diagrams and the existing known equivalences between certain logics, formal language theory classes and some automata to inform the development of diagrammatic logics. Such developments could have many advantages, one of which would be aiding software engineers who are familiar with formal languages and automata to more intuitively understand diagrammatic logics. In this paper we consider relationships between spider diagrams of order (an extension of spider diagrams) and the star-free subset of regular languages. We extend the concept of the language of a spider diagram to encompass languages over arbitrary alphabets. Furthermore, the product of spider diagrams is introduced. This operator is the diagrammatic analogue of language concatenation. We establish that star-free languages are definable by spider diagrams of order equipped with the product operator and, based on this relationship, spider diagrams of order are as expressive as first order monadic logic of order.

Modelling Secure Cloud Computing Systems from a Security Requirements Perspective

This paper presents a cloud modelling language for defining essential cloud properties, enabling the modelling and reasoning about security issues in cloud environments from a requirements engineering perspective. The relationship between cloud computing and security aspects are described through a meta-model, aligning concepts from cloud computing and security requirements engineering. The central concept of the proposed approach is built around cloud services, where the propagation of relationships from a social perspective, abstract software processes and the foundational infrastructure layer are captured. The proposed concepts are applied on a running example throughout the paper to demonstrate how developers are able to capture and model cloud concepts across multiple conceptual layers, facilitating the understanding of cloud security requirements and the design of security-embedded cloud systems to realise organisational needs.

Combining Sketching and Traditional Diagram Editing Tools

The least cognitively demanding way to create a diagram is to draw it with a pen. Yet there is also a need for more formal visualizations, that is, diagrams created using both traditional keyboard and mouse interaction. Our objective is to allow the creation of diagrams using traditional and stylus-based input. Having two diagram creation interfaces requires that changes to a diagram should be automatically rendered in the other visualization. Because sketches are imprecise, there is always the possibility that conversion between visualizations results in a lack of syntactic consistency between the two visualizations. We propose methods for converting diagrams between forms, checking them for equivalence, and rectifying inconsistencies. As a result of our theoretical contributions, we present an intelligent software system allowing users to create and edit diagrams in sketch or formal mode. Our proof-of-concept tool supports diagrams with connected and spatial syntactic elements. Two user studies show that this approach is viable and participants found the software easy to use. We conclude that supporting such diagram creation is now possible in practice.

What can concept diagrams say

Logics that extend the syntax of Euler diagrams include Venn-II, Euler/Venn, spider diagrams and constraint diagrams, which are first-order. We show that concept diagrams can quantify over sets and binary relations, so they are second-order. Thus, concept diagrams are highly expressive compared with other diagrammatic logics.

Modelling secure cloud systems based on system requirements

We enhance an existing security governance framework for migrating legacy systems to the cloud by holistically modelling the cloud infrastructure. To achieve this we demonstrate how components of the cloud infrastructure can be identified from existing security requirements models. We further extend the modelling language to capture cloud security requirements through a dual layered view of the cloud infrastructure, where the notions are supported through a running example.