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EPSRC grant EP/I005943/1 : Southampton, Durham, King's, Loughborough, Newcastle, UEL, York : Oct 2010 -- Sept 2013
York PI: Jon TImmis
RA: Paul Andrews

What will the UK's critical infrastructure look like in 2030? In 2050? How resilient will it be? Decisions taken now by policy makers, NGOs, industrialists, and user communities will influence the answers to these questions. How can this decision making be best informed by considerations of infrastructural resilience? This project will consider future developments in the UK's energy and transport infrastructure and the resilience of these systems to natural and malicious threats and hazards, delivering a) fresh perspectives on how the inter-relations amongst our critical infrastructure sectors impact on current and future UK resilience, b) a state-of-the-art integrated social science/engineering methodology that can be generalised to address different sectors and scenarios, and c) an interactive demonstrator simulation that operationalises the otherwise nebulous concept of resilience for a wide range of decision makers and stakeholders.

White Rose University Consortium : York/Leeds/Sheffield: Oct 2010 -- Sep 2013
York PI: Jon Timmis

Dysregulation of inflammatory responses underlies diseases such as arthritis and atherosclerosis. Moreover, activation of the inflammatory transcription factor NF-kB has recently been identified as a significant parameter in determining tumour development. Detailed information of fundamental events directing signal amplification and potentiation of the NF-kB pathway will therefore be of significance in understanding mechanisms of inflammatory control which underlie some of the most common diseases of the 21st century. This project employs agent-based modelling to explore a pathway of the innate immune system with a combined modelling and experimental approach, using modelling to help drive in-vitro experimentation and give crucial insight into regulatory effects. This work will contribute to the development of computational models of the role of the NF-kB pathway, which can be tested experimentally, and also to the area of computer science and the use and development of such modelling techniques.

EPSRC grant EP/G043604/1 : York, Brunel : Jun 2009 -- May 2013
PI: John A Clark

Misunderstanding the semantics of descriptive notations is a common source of problems in software development. We believe that these misunderstandings can be represented as semantic mutants over descriptions and that test data produced to kill semantic mutants is effective at finding faults caused by such misunderstandings: It will often find faults that are typically missed by test sets produced by extant testing strategies (and in particular, by test sets that are produced to kill traditional syntactic mutants). We also believe that he production of semantic mutants and the generation of test data to kill them can be automated.

Gatsby Foundation grant : Biology/CS : Jan 2009 -- Dec 2013
PI: Ottoline Leyser
CI: Susan Stepney

This project aims to improve our understanding of the relationship between phenotype, its plasticity, and its robustness, using the hormonal control of shoot branching in Arabidopsis under high and low nitrogen supply as a model system. The 5 year programme builds on existing work on the molecular mechanisms controlling shoot branching and their modelling and simulation, and integrates both these aspects to explore systems properties using the new population genetics tools. Modelling aspects are in collaboration with Przemyslaw Prusinkiewicz (Calgary) and population genetics aspects are in collaboration with Paula Kover (Manchester).

EPSRC grant EP/F062192/1 : York (Electronics/CS), UWE : Oct 2008 -- Sept 2011
PI: Andy Tyrrell
CIs: Gianluca Tempesti, Jon Timmis
RA: Jerry Liu
RS: Omer Qadir

The objective of this research is to evaluate and apply novel, biologically inspired, processes and algorithms for building reliable VLSI systems on silicon that possess self-diagnostic and self-healing properties. Inspired by nature, our research will adapt properties of biological systems, such as their multi-cellular organisation and evolutionary development, to create efficient electronic systems. It will also apply biological processes and the characteristics of both the innate and the acquired immune system to help solve the reliability and fault tolerant issues of artificial systems at cell, tissue (subsystem) and also at organism (system) levels. Our research will aim to pave the way for a biologically inspired unique design approach for electronics systems across a wide range of applications; from communication, through computing and control, to systems operating in hostile environments.

EPSRC grant EP/F060041/1 : York (Electronics/CS/Biology): Sept 2008 -- Aug 2013
PI: Andy Tyrrell
CIs: Susan Stepney, Leo Caves
RA: Mic Lones
RS1, RS2: Alex Turner, Luis Fuente

Previous work by ourselves and others has shown how the structure and organisation of biological organisms can motivate the design of computer hardware and software, with the aim of capturing useful properties such as complex information processing and resistance to environmental perturbation. This project focuses upon one of the most complex sets of structures found in biological systems: biochemical networks. These structures are fundamental to the development, function and evolution of biological organisms, and are the main factor underlying the complexity seen within higher organisms. Previous attempts to build hardware and software systems motivated by these structures has led to a group of computer architectures which we collectively refer to as artificial biochemical network models. The best known of these is the artificial genetic network, which has shown itself to be an effective means of expressing complex computational behaviours, particularly within robotic control. Nevertheless, this field of research has received relatively little attention, and little is known about the computational properties of these architectures. The aim of the proposed work is to develop better artificial biochemical network models, which we will do by both bringing together existing work and introducing new understanding from the biological sciences. We will also develop a theoretical framework to better understand what these computational architectures are capable of, and show how how these models can be applied to the difficult problem of controlling a robot in real world environments. It is expected that this work will also produce insights into the function and evolution of the biological systems on which the architectures are modelled.

EPSRC grant EP/F031033/1 : York (CS/Electronics/Biology): Jun 2008 -- Dec 2011
PI: Susan Stepney
CIs: Tim Clarke, Peter Young
RAs: Simon Hickinbotham, Ed Clark
RSs: Adam Nellis, Mungo Pay

PLAZZMID is a novel flexible and extensible computational framework and toolset inspired by sophisticated models of complex biological evolutionary processes that occur in bacteria and in bees. The tools will be able to be used both to build and analyse testable models of biological evolutionary processes, and to build and analyse powerful novel computational metaphors and algorithms based on these more sophisticated biological models. Within the research project, the tools will be used in a series of theoretical biological experiments on the relationship between genome structure and evolvability, and used to evolve computational systems exhibiting complex homeostatic control in a changing environment.

EU FP7 grant 216342 : Feb 2008 -- Jan 2013
York PI: Jon Timmis
CI: Andy Tyrrell

The main focus of this project is to investigate and develop novel principles of adaptation and evolution for symbiotic multi-robot organisms based on bio-inspired approaches and modern computing paradigms. Such robot organisms will consist of super-large-scale swarms of robots, which can dock with each other and symbiotically share energy and computational resources within a single artificial-life-form. When it is advantageous to do so, these swarm robots can dynamically aggregate into one or many symbiotic organisms and collectively interact with the physical world via a variety of sensors and actuators. The bio-inspired evolutionary paradigms combined with robot embodiment and swarm-emergent phenomena, enable the organisms to autonomously manage their own hardware and software organization. In this way, artificial robotic organisms become self-configuring, self-healing, self-optimizing and self- protecting from both hardware and software perspectives.

EPSRC grant EP/F032749/1 : York (Biology/Maths/CS/Electronics/Chemistry): Jan 2008 -- Jan 2011
PI: Leo Caves
CIs: Gustav Delius, Angelika Sebald, Susan Stepney, Jon Timmis, Jamie Wood

At the University of York we are identifying mutual/synergistic research interests across disciplines. We are now taking the next step and moving towards collaborative cross-disciplinary research. TRANSIT (TRANSition from Interdisciplinarity to Transdiciplinarity) is a bridging programme to nurture this nascent collaborative research culture. The TRANSIT programme provides the resources to promote staff awareness and interaction through a range of physical and virtual fora. At the heart of TRANSIT we provide the time, space and support for the creative thinking and collaboration necessary for the generation and evaluation of novel cross-disciplinary concepts and ideas. To then develop these ideas, TRANSIT provides resources to fund short, focussed feasibility studies, with the aim of generating the proof of principle and initial results, leading towards the submission of competitive research proposals. The goal is to promote further interdisciplinarity at York, and to move towards the development of a true collaborative transdisciplinary research culture.

EPSRC grant EP/F005881/1 : York, Newcastle, Glasgow : May 2008 -- Apr 2011
PI: Sam Braunstein

Quantum computation is based on computers which operate on the level of quantum mechanics rather than classical electronics. The advantage of this is that in quantum mechanics entities can be simultaneously in many different positions at once: and this allows states of a quantum computer to behave in some ways like a stack of parallel states. This parallel stack does not unfortunately come without strings and, because of the physics of quantum mechanics, it is very difficult to find out what is in any such stack at a particular time: so reading the output of a quantum computer is not easy. Some powerful quantum algorithms have been developed: for example by Shor to factor integers much faster than convential algorithms can. However the number of such algorithms that we know is not growing very rapidly. One reason for this is that we do not have a systematic understanding of how to build up quantum computing algorithms and indeed do not have a comprehensive library of algorithms for very basic functions and procedures for building from them. The main aims of this project are to construct such a systematic foundation for quantum computation and to establish procedures for basic processes. We shall test our success in these objectives by attempting to construct algorithms for problems which arise in group theory. This area of mathematics provides an endless array of algorithmic problems at all levels of difficulty, so is a good test bed for a potential computation system. We shall also consider how to extend the analysis of cryptographic systems from classical schemes to quantum schemes. In particular this is expected to allow us to build an automated voting process which cannot be tampered with or broken into by the people who run it.

The overall project involves 1 Research Associate (at York), and 1 Research Student (at Newcastle).

EPSRC grant EP/E053505/1 : Kent, York (CS/Electronics/Chemistry) : Oct 2007 -- Mar 2012
PI: Susan Stepney
CIs: Fiona Polack, Jon Timmis, Andy Tyrrell
RA: Paul Andrews
RSs: Teodor Ghetiu, Tim Hoverd, Antonio Gomez Zamorano, Jenny Owen

This work builds capacity in generic modelling tools and simulation techniques for complex systems, to support the modelling, analysis and prediction of complex systems, and to help design and validate complex systems. Drawing on our state-of-the-art expertise in many aspects of computer systems engineering, we will develop CoSMoS, a modelling and simulation process and infrastructure specifically designed to allow complex systems to be explored, analysed, and designed within a uniform framework.

The overall project involves 2 Research Associates (1 at York, 1 at Kent), and 6 Research Students (4 at York, 1 funded by Microsoft Research; 1 at Kent).

EPSRC grant EP/F00334X/1 : York (CS: RTS/NSC groups) : Oct 2007 -- Mar 2011
PI: Iain Bate
CIs: John A Clark, Dimitar Kazakov

Reasoning about the timing properties of many modern systems is crucial. Examples include anti-lock braking systems, air traffic control systems, and even medical applications such as X-ray dosage delivery equipment. Reasoning about response times of such systems has been the subject of much research. In particular, a great deal of scheduling theory has been developed to provide bounds on worst-case response times. Such work assumes the timing properties of individual components in the system are well understood. In particular, the Worst Case Execution Time (WCET) for an individual task is an input to all forms of real-time scheduling theory. The derivation of such WCETs therefore underpins our efforts to guarantee response times in critical systems. The real-time systems community recognizes this as a major challenge.

Several researchers have identified measurement-based approaches as a promising candidate to cope with modern-day engineering demands. However, relying only on measurements to infer WCET bounds in a black box approach is regarded as unsound by most researchers. We need information to reason effectively about WCETs, but this is not readily available. Measurements however, can be taken freely. The weakness of measurement is ensuring the results are safe. Thus, rather than directly inferring bounds on WCETs from execution trace timings, why not use the measurements to infer a model of the underlying system that can form an input into further WCET calculations? Our proposal addresses this very question. Since the problem is in essence a learning problem, we propose to investigate how well leading edge machine learning approaches can be adopted or adapted to this end.

EPSRC grant EP/D050618/1 : King’s College London, York, Birmingham : June 2006 -- Dec 2011
PI: John A Clark
CI: Iain Bate

Current software engineering practice is a human-led search for solutions which meet needs and constraints under limited resources. Often there will be conflict, both between and within functional and non-functional criteria. Naturally, like other engineers, we search for a near optimal solution. As systems get bigger, more distributed, more dynamic and more critical, this labour-intensive search will hit fundamental limits. We will not be able to continue to develop, operate and maintain systems in the traditional way, without automating or partly automating the search for near optimal solutions.

Automated search based solutions have a track record of success in other engineering disciplines, characterised by a large number of potential solutions, where there are many complex, competing and conflicting constraints and where construction of a perfect solution is either impossible or impractical. The EPSRC SEMINAL network demonstrated that these techniques provide robust, cost-effective and high quality solutions for several problems in software engineering. Successes to date can be seen as strong pointers to search having great potential to serve as an overarching solution paradigm.

SEBASE aims to provide a new approach to the way in which software engineering is understood and practised. It will move software engineering problems from human-based search to machine-based search. As a result, human effort will move up the abstraction chain, to focus on guiding the automated search, rather than performing it. This project will address key issues in software engineering, including scalability, robustness, reliability and stability. It will also study theoretical foundations of search algorithms and apply the insights gained to develop more effective and efficient search algorithms for large and complex software engineering problems. Such insights will have a major impact on the search algorithm community as well as the software engineering community.

The overall project involves 6 Research Associates, 6 Research Students and a dedicated Programme Manager. At York the work is a collaboration between the Non-Standard Computation and Real-Time Systems groups.

York (CS/Electronics), Kent, NCR : Oct 2005 -- Oct 2011
Jon Timmis

There is currently an increased awareness within the public about the potential of fraud in financial services, especially with the well publicised ATM fraud attacks. This has lead to an increased requirement for additional sensing in the ATM to detect these types of attack. This requires intelligence to be built into the system to allow more efficient processing of the new complex data that is available in the ATM. The intelligence uses "sensor fusion" to amalgamate the data and process it to produce more accurate alarm messages to the ATM network control system. This project aims to provide the intelligence for the processing of the sensor data allowing the raw data to be converting into more accurate and complete alarm messages that can be passed into the management and fraud detection systems.

UKCRC Grand Challenge 7 : 2003 -- 2023...?
Susan Stepney, Sam Braunstein, John A Clark, Jon Timmis

A 20 year research challenge, to produce a fully mature science of all forms of computation, that unifies the classical and non-classical paradigms

 Past projects