Professor Jon Timmis : Artificial Immune Systems Research

Prof Jon Timmis
Department of Computer Science and Department of Electronics
University of York
Heslington, York. YO10 5DD
Tel +44 (0) 1904 322318/325361 
Email: jon (dot) timmis (at) york (dot) ac (dot) uk 


Quick links to my: Research Publications Teaching Admin Misc.


From August 2013 I have moved full-time to the Department of Electronics here at York. I no longer maintain these pages so please take a read of my new pages.


I am Professor of Intelligent and Adaptive Systems and hold a joint appointment between the Department of Computer Science and the Department of Electronics . I am a member of the Non Standard Computation group, the Intelligent Systems group and the York Centre for Complex Systems Analysis (YCCSA). I am also a member of the York Computational Immunology Lab

I am running a new MSc in Autonomous Robotics Engineering, starting in 2013.

Research

My work cuts across many areas, but most of my work revolves around immunology, either developing computational models of immune function (computational immunology), or fault-tolerance achieved via bio-inspired engineering with a focus on the immune system (immuno-engineering). In terms of applications, I focus mainly on swarm robotic systems as a platform for testing our ideas realting to fault tolerence and anomaly detection. My wider interests are in modelling and simulation of complex systems.

Take a read of the Computational Immunology Lab website for more information on our work in that area.

I currently hold a Royal Society Wolfson Research Merit Award where my work is focussed on computational immunology and self-healing swarm robotic systems. I work on a variety of robotic platforms, we made a video for some fun, of our flying robots (make sure the volume is turned up).

I am Visiting Professor at the Universiti Kebangsaan Malaysia.

A few years ago, Nature did a piece on AIS, take a read

If you want to know more about AIS, I have written a few papers that you might find interesting all with pre-final version PDFs provided for you (you can find the full reference for citation purposes on my publication page):

  • On Artificial Immune Systems and Swarm Intelligence. J. Timmis, E. Hart and P. Andrews . Swarm Intelligence (2010). Here we explore how AIS can be considered in the context of SI, and importantly, how the two approaches can be used in a complimentary manner.
  • Immuno-engineering. J. Timmis, E. Hart, A. Hone, M. Neal, A. Robins, S. Stepney and A. Tyrrell. A position on a new approach to developing immune-inspired systems, in a more principled manner.(2008)
  • Theoretical Advances in Artificial Immune Systems J. Timmis, A. Hone, T. Stibor and E. Clark. A review of the theoretical side of AIS. This paper has been rated in the top 5 hottest papers for TCS-C since August 2008.
  • An Interdisciplinary Perspective on Artificial Immune Systems J. Timmis, P. Andrews, N. Owens and E. Clark. Provides a review of AIS taking into account interactions between immunology and computer science and engineering.(2008)
  • Application Areas of AIS: Past Present and Future. E. Hart and J. Timmis. Provides a review of the application side of AIS, and discusses the types of applications that AIS might be more suited to. (2008)
  • Artificial Immune Systems: Today and Tomorrow. J. Timmis. Provides my thoughts on what was wrong with AIS at that time and how we might work towards fixing the issues. (2007)
  • I have recently helped to guest edit a number of special issues on AIS:
  • Special Issue on Advances in Artificial Immune Systems, in the journal Evolutionary Intelligence Vol. 4(2). 2011. Emma Hart, Chris McEwan, Jon Timmis and Andy Hone.
  • Special issue on the interaction between computation and biology. Jon Timmis, Paul S. Andrews, Susan Stepney. Natural Computing Vol 10(1). 2011.
  • Special Issue on Theoretical Aspects of Artificial Immune Systems, Journal of Theoretical Computer Science Vol 412, Issue 6, Pages 499-560. 2011. Jon Timmis, Paul Andrews and Andy Hone.
  • Special Issue on Artificial Immune Systems, Swarm Intelligence Vol 4, Number 4, 2010. Jon Timmis, Paul Andrews and Emma Hart.
  • Jobs and Studentships

    None at present.

    Research Activities

    Current Research Council Projects

  • SYMBRION. A collective robotics project funded by the EU. We are developing the immune system for the robotic units and collectives.
  • CoCoRo. Collective Cognitive Robotics, again funded by the EU. We are developing the operating systems and middleware that has inbuilt artificial immune systems, and also developing a swarm-based recovery strategy based on T Regulatory networks.
  • CoSMoS. Complex Systems modelling and simulation, funded by the EPSRC.
  • Resilent Futures. Complex systems modelling project developing simulations for stakeholders in the transport and energy industries.
  • Ecosystem Interactions. Funded by DEFRA. Collaboration with Prof Piran White, Dave Raffaelli, Environment Department at York, and Prof Stuart Bell, Law Department at York.
  • Current Industrial Funding

    I hold two current research grants from a major manufacture of electro-mechanical devices where we develop ideas for dynamic data fusion.

    I hold a grant from DSTL on chemical agent detection deployed on robotic platforms.

    I hold a grant from Syngenta to develop a decision support tool for farmers to optimise bird life diversity on their land.

    Activities

  • I run the AIS website that contains AIS code, teaching material, news and events and more for AIS.
  • I was heavily involved in the creation of the International Conference on Artificial Immune Systems (ICARIS). Please see the ICARIS webpage for more information. I am now the chair of the ICARIS steering committee.
  • Check out the web site for more information on the first text book dedicated to Artificial Immune Systems, authored by myself and Leandro de Castro. Artificial Immune Systems: A New Computational Intelligence Approach from Springer-Verlag. See it on Amazon here . A review of the book is here in Neural Networks the on-line version of the journal.
  • I am on the Grand Challange 7 commitee, part of the Grand Challenges for Computing Research .
  • I am a Senior Member of the IEEE and a member of the SMC Industrial Applications Technical Committee.
  • I am on the editorial board of Journal of Theoretical Computer Science
  • I am on the editorial board of Evolutionary Intelligence
  • I am on the editorial board of Natural Computing
  • I am Associate Editor of the International Journal of Artificial Life Research
  • I am Associate Editor of the International Journal of Natural Computing Research
  • Books

    In Silico Immunology

    Darren R. Flower, Jon Timmis, editors, in silico Immunology

    Overview: Immunology is an all important science, addressing as it does, the most pressing medical needs of our time: infectious disease and transplantation medicine. It has given us vaccines on the one hand and therapeutic antibodies on the other. After a century of emperical research, it is now poised to finally reinvent itself as a quantitative, genome-based science.
    Theoretical immunology is the application of mathematical modeling to diverse aspects of immunology ranging from T cell selection in the Thymus to the epidemiology of vaccination. Immunoinformatics, the application of computational informatics to the study of immunological macromolecules, address important questions in immunobiology and vaccinology. Artificial Immune Systems (AIS) is an area of computer science which uses ideas and concepts from immunology to guide and inspire the development of new algorithms and architectures.
    These three different disciplines-theoretical immunology, immunoinformatics and AIS are now poised to engineer a paradigm shift from hypothesis- to data-driven research, with new understanding emerging from the analysis of complex datasets. in silico immunology will summarize these emergent disciplines and, while focusing on cutting edge developments, will address the issue of synergy as it shows how these three are set to transform immunological science and the future of health care. See it on-line using the doi link 10.1007/978-0-387-39241-7

    Leandro de Castro and Jon Timmis, Artificial Immune Systems: A New Computational Intelligence Approach

    Overview: Over the past few decades there has been a growing interest in the use of biology as a source of inspiration for solving computational problems. This area of research is often referred to as Biologically Inspired Computing. The motivation of this field is primarily to extract useful metaphors from natural biological systems, in order to create effective computational solutions to complex problems in a wide range of domain areas. The more notable developments have been the neural networks inspired by the working of the brain, and the evolutionary algorithms inspired by neo-Darwinian theory of evolution. More recently however, there has been a growing interest in the use of the biological immune system as a source of inspiration to the development of these computational systems. The immune system contains many useful information-processing abilities, including pattern recognition, learning, memory and inherent distributed parallel processing. For these and other reasons, the immune system has received a significant amount of interest to use as a metaphor within computing. This emerging field of research is known as Artificial Immune Systems (AIS). Essentially, AIS are the use of immune system components and processes as inspiration to construct computational systems. AIS is very much an emerging area of biologically inspired computation and has received a significant amount of interest from researchers and industrial sponsors in recent years. Applications of AIS include such areas as machine learning, fault diagnosis, computer security, scheduling, virus detection, and optimisation. The field of AIS is showing great promise of being a powerful computing paradigm and therefore the writing of this book is very timely. The book will present a general introduction to the field of immunology, stressing the key areas that are currently used within the field of AIS. A framework for engineering AIS is then introduced to the reader, followed by an up to-date review of the state of the art in AIS, in then light of that framework. It is hoped that through these initial chapters the reader will become aware of the powerful metaphor of the immune system and be left with a concrete set of ideas of how to create their own AIS. The book then goes onto describing the natural immune system in context with other biological systems and explores interaction between those systems. This will allow the reader to develop an understanding and appreciation for the richness of biology and its possible inspiration. This is then followed by a discussion of the field of AIS in relation to other computational intelligence paradigms. It is hoped that this chapter will allow the reader to become familiar with other techniques and understand the relative strengths and weaknesses of each and where the use of each (including AIS) would be appropriate.

    Current Research

    My work cuts across many areas, but most of my work revolves around immunology, either developing computational models of immune function (computational immunology), or fault-tolerance achieved via bio-inspired engineering with a focus on the immune system (immuno-engineering) In terms of applications, I focus mainly on swarm robotic systems as a platform for testing our ideas. My wider interests are in modelling and simulation of complex systems.

    Below is a current list of people, that in one way or another, work with me.

    Computational Immunology

    See lab website for more information on this area and the people.
  • James Butler
    James is a PhD student on the DTC on Regenerative Medicine and is working with myself and Mark Coles on B cell follicle development. James is based at the Centre for Immunology & Infection (CII, run jointly by the Department of Biology and the Hull York Medical School).
  • Bjorn Gerckens
    Simulation Modelling of mAb Efficacy for the Treatment of Autoimmune Disease (CASE)
    Bjorn is a PhD student on the DTC in Regenerative Medicine and is working with myself and Dr Mark Coles on computational models and simulations of auto-immune diseases, in collaboration with a major pharmaceutical company. Bjorn is based at the Centre for Immunology & Infection (CII, run jointly by the Department of Biology and the Hull York Medical School).
  • Stephanie Dyson
    Systems biology approach to understand inflammation mechanisms active in the gastrointestinal tract
    Steph is a PhD student funded by the BBSRC and a major pharmaceutical company and is working with myself and Dr Marika Kullberg in the CII, and is working on developing agent-based models of Crohn's disease. Steph is based at the Centre for Immunology & Infection (CII, run jointly by the Department of Biology and the Hull York Medical School).
  • Dr. Richard Greaves
    Tool Chains for Modelling and Simulation of the Immune System
    Richard is a research associate working with myself and Dr Mark Coles developing our tool chain for modelling the simulation of immunological function, with a focus on auto-immune diseases. Richard is based in Computer Science.
  • German (Johnny) Leonov
    Modelling MicoRNA
    Johnny is a PhD on the Wellcome Trust funded CIDCATS programme working with Dr Dimitris Lagos and myself on understanding the role of mircoRNA regualtory networks using a combined experimental and computational approach. Johnny is based in the CII
  • Daniel Moyo
    Computational Modelling of Granuloma Formation
    Daniel is a PhD student developing models of early events in the formation of granulomas in the context of Leichmania, in collaboration with Paul Kaye in the CII. Daniel is based in Computer Science.
  • Dr. Mark Read
    Computational Modelling of T-regulatory Cells and self-repairing swarm systems
    Mark is a research associate and is interested in developing computational models of T-regulatory cells. We are working with Vipin Kumar of Torry Pines Institute For Molecular Studies. Mark is now based in Electronics and is working as an RA for myself and Andy Tyrrell on the EU funded project CoCoRo which is concerned with developing novel bio-inspried approaches to fault tolerence in underwater swarm robotic systems. This combines his modelling work in EAE with swarm robtoic systems.
  • Richard Williams
    Computational modelling of NF-κ&beta pathway. Richard is a PhD student and part of a White Rose Network on Immune System modelling, and is co-supervised by Prof Eva Qwarnstrom at the Medical School at Sheffield. Richard is based in Computer Science.
  • Complex Systems

  • Paul Andrews
    Resilient Futures. Paul is a research associate working on this EPSRC funded project and is developing the final interactive demonstration system that integrates various agent-based and network-based models for stakeholder engagement to support decision making for national critical infrastructure.
  • Bio-Inspired Engineering

  • Anna Ladi
    Automated Chemical Identification
    Anna is working on developing adaptive detection technqiues that can be deployed in a real-time, robotic system for the detection of molecular signatures.
  • Dr. James Hilder
    Immune-inspired operating systems and middleware for swarm robotic systems
    James is a research asociate and is working on the CoCoRo project with myself and Andy Tyrrell and is developing all the low-level software for the robotic platforms (underwater robots!).
  • Becky Naylor
    Self Repairing Strategies for SYMBRION robotic systems.
    Becky is working on developing self-repair approaches in the SYMBRION robotic systems. Her work will integrate the detect, diagnose and recovery processes in the swarm and modular robotic units. Becky is a research associate in the Electronics department and works with myself and Andy Tyrrell.
  • Paul Taylor
    Autonomic Business Processes
    Paul is working on his EngD with myself and Fiona Polack, whilst working at BT as a researcher.
  • Colin Bonney
    Self-reconfigurable hardware:
    Colin is a PhD student co-supervised with Dr Gianluca Tempesti and is investigating immune-inspired approaches to reconfigurable processor architectures. Colin is based in Electronics.
  • Lim Tiong Hoo
    AIS and Sensor Networks
    Tiong is a PhD student looking at the the application of AIS in sensor networks. Tiong is based in Computer Science and is co-supervised by Iain Bate
  • Xiaohu Liu
    Dynamic Data Fusion for Mobile Devices
    Building on the work of Piero, Liu is a PhD student developing on-line recommender systems. Liu is based in Electronics and co-supervised by Dr Rogerio de Lemos
  • Lachlan Murray
    Fault Tolerance in Collective Robotic Systems
    Lachlan is an RA working on the SYMBRION project. He is co-supervised by Andy Tyrrell and is in the Electronics Department.
  • Alan Millard
    Self-Healing Swarm Robotic Systems
    Alan is working on developing approaches to recovery from failures in swarm robotic systems and is co-supervised by Prof Alan Winfield from Bristol Robotics Laboratory.
  • James Stovold
    Cogntive Swarm Systems
    James is working with myself and Dr Simon O'Keefe investigating cognition within swarm systems, and swarm robtoic systems. James is based in Computer Science.
  • PhD students writing up

  • Lachlan Murray
    Fault Tolerance in Collective Robotic Systems
    Lachlan is a PhD student working on the SYMBRION project looking at immune approaches to fault tolerance in collective robotic systems. He is co-supervised by Andy Tyrrell and is in the Electronics Department.
  • Submitted

  • Jenny Owens
    Evolutionary Swarm Robotics
    Jenny is a PhD student working on the CoSMoS project investigating the modelling and simulation of swarm robotic systems. She is co-supervised with Prof Susan Stepney and Prof Alan Winfield from Bristol Robotics Laboratory.
  • Piero Conca
    Adaptive Data Fusion with AIS
    In collaboration with NCR. Co-supervised with Dr. Rogerio De Lemos at the University of Kent. Piero is based in Electronics.
  • NuralHuda Mohd Azmi
    AIS and Information Filtering
    Huda is a PhD student investigating the application of AIS to information filtering and web-mining and the development of of novel AIS based on modelling aspects of the immune system . She is co-supervised by Dr Fiona Polack and is based in Computer Science and is aligned with the CoSMoS project.
  • Old Projects
  • SABRE: Self Healing Cellular Architectures for Biologically-inspired highly Reliable Electronic Systems. Funded by EPSRC from October 2008 to September 2011.
  • An Extensible Architecture for Homeostasis in Electronic Systems. A 3 year project that investigated homeostasis in electronic systems and the use of T-cell signalling for anomaly detection.
  • Bioinformatics, Immunology and Algorithms make Short work of PROtein Function claSsification. A 2.5 year project that developed various hierical methods for GPCR classification.
  • Past Students/RA's

    Below is a list of people, who I am pleased to say survived working with me!

    Research Associates

  • Carl Ritson. Carl worked on a DEFRA project, developing stakeholder tools for ecosystem services.
  • Dr Kieran Alden. Kieran did his PhD, then a post-doc before leaving for the University of Birmingham, in Jan 2013.
  • Adam Nellis. Adam was a research assoiciate working on developing a tool to help farmers make informed decisions about optimal usage of land to maximise birld life diversity. The project was funded by Syngenta.
  • Dr Yang Liu (Jerry). Jerry worked on the SABRE project from October 2008 to Sept. 2011 and also undertook his PhD with me from 2005 to 2008.
  • Dr Maizura Mohktar. Mai worked on the SYMBRION project until Feb. 2010
  • Dr Andy Greensted who was an RA on An Extensible Architecture for Homeostasis in Electronic Systems which ended in September 2009.
  • Dr Miguel Mendao, who was an RA on the BIASPROFS project that ended in November 2008.
  • Graduate Research Students

    Completed (some awaiting final CRC of thesis):
    1. Dr. Kieran Alden. Modelling and Simulation of lyphoid tissue organogenesis. (Biology). 2012.
    2. Dr. Antonio Zamorano. Complex Systems Simulation, design and implementation using FPGAs. (Electronics). 2012.
    3. Dr.Ran Bi. Immune-inspired fault diagnosis for a robotic system. (Electronics) 2012.
    4. Dr. Lau Hui Keng (Kelvin). Error Detection in Swarm Robotics: A Focus on Adaptivity to Dynamic Environments. (Computer Science) 2012.
    5. Dr. Ameila Ismail (Rita). Immune-inspired Self Healing in Swarm Robotic Systems. (Computer Science) 2012.
    6. Dr. Omer Qadir. Protien Processor Associate Memory. (Electronics) 2011.
    7. Dr Mark Read. Statistical and Modelling Techniques to Build Confidence in the Investigation of Immunology through Agent-Based Simulation. (Computer Science). 2011.
    8. Dr. Richard Greaves. Computational Modelling of Treg Networks in Experimental Autoimmune Encephalomyelitis. (2011) (MSc by Research)
    9. Dr Nick Owens. From Biology to Algorithms. (Electronics). 2010.
    10. Dr Luca Albergante (Milan). A Petri Net Model of Liver Response to Visceral Leishmaniasis: self-regulation and complex interplay in the vertebrate immune system. (Mathematics) 2010.
    11. Dr Adam Knowles Immunologically Inspired Data Fusion for Anomaly Detection in Electromechanical Systems PhD. (Electronics). 2010. Thesis commercially sensitve and is unavailable
    12. Dr Yang Liu A Neuro-Immune Inspired Computational Framework and its Applications to a Mchine Visual Tracking System PhD. (Electronics) 2010. PDF of thesis
    13. Dr Ed Clark A Framework for modelling stochastic optimisation algorithms with Markov chains. PhD. (Electronics) 2009. PDF of thesis
    14. Dr Paul AndrewsAn Investigation oor the Development of Artificial Immune Systems: A Case-Study in Immune Receptor Degeneracy PhD. (Computer Science) 2009. PDF of thesis
    15. Dr. Peter May. An Artficial Immune System Approach to Mutation Testing Test Data Generation PhD. (Computer Science) 2006.
    16. Dr. Andy Secker. Artificial Immune Systems for Web Content Mining: Focusing on the Discovery of Interesting Information PhD. (Computer Science) 2006. Thesis .
    17. Dr. Modupe Ayara. An Immune Inspired Approach For Adaptable Error Detection in Embedded Systems PhD. (Computer Science) 2005.
    18. Dr. Andrew Watkins. Exploiting Immunological Metaphors in the Development of Serial, Parallel and Distributed Learning Algorithms PhD. (Computer Science) 2005.PDF of thesis
    19. Dr. Tom Knight. MARIA: A Multilayered Unsupervised Machine Learning Algorithm Based on the Vertebrate Immune System PhD. (Computer Science) 2005.download PDF of thesis
    20. Dr Giuseppe Nicosia (Catania, Italy). Immune Algorithms for Optimisation and Protein Structure Prediction, (Mathematics and Computer Science) 2004.
    21. Johnny Kelsey. An Immune Inspired Algorithm for Function Optimisation . MSc by Research (Computer Science). 2004.

    Other Collaborations

    I was a Visiting Professor at the Helsinki University of Technology, Finland, in the Power Electronics Laboratory. I was also a Visiting Professor at the University of Technology, Malaysia. I work with Vipin Kumar at TPIMS, Paul Kaye and Mark Coles of the CII here at York and Prof Eva Qwarnstrom at Sheffield on various aspects of immune system modelling.

    Research Opportunities


    I have many possibilities for research topics centred around the area of Artificial Immune Systems and homeostatic systems. Given my joint appointment, some topics for PhD are more suitable for Computer Science and others for Electronics candidates:

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    Publications

    For my full list of published papers (most with PDF's) see here.

    For a Google powered list (which is very up to date) then see my Google Scholar page .

    Papers Recently Submitted

    Journal Papers
  • A Petri Net model of granulomatous inflamation predicts an important role for Kupffer cell-derived IL-10 in the control of experimental visceral leishmaniassis. L. Albergante, J. Timmis, L. Beattie and P.Kaye Submitted to Plos Comp Bio.
  • Demonstrating the dependability of a routing protocol using statistical approaches. T. H. Lim, I. Bate and J. Timmis Submitted to IEEE Transactions on Computers.
  • Determining cellualr interactions and interention in inflammatory disease using a spatially resolved model M. Read, P. Andrews, J.Timmis, R. Williams, R. Greaves, Y. Sheng, M. Coles and V. Kumar Submitted to Plos ONE
  • Conference Papers
    Book Chapters
  • Evolvable Robot Hardware. A. Winfield and J. Timmis.
  • Papers in Preperation

    Journal Papers

    Book Chapters

    Conference Papers

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    Teaching

    In Computer Science I currently teach on the following courses:
  • Swarm Intelligence
  • I have one MEng student, Magnus Trip, who is looking into automated callibration of agent-based simulations of immune function.
  • In Electronics for 2012/13 I am not teaching in the department, excepting I have one MEng student, Sophie Alexander, working on underwater swarm robotics.

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    Admin

  • I am chair of the Research Committee in Electronics. (Head of Research)
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    Misc.

  • For sanity, I check out the Dilbert site