Conference Papers

Choosing and adapting design notations in the principled development of complex systems simulations for research. Fiona A. C. Polack, In Modelling the Physical World Workshop, at Models 2012, Innsbruck, Austria, October 2012. ACM Digitial Library

Multiple model simulation: modelling cell division and differentiation in the prostate. Alastair Droop, Philip Garnett, Fiona A. C. Polack and Susan Stepney. In Proceedings of the 2011 Workshop on Complex Systems Modelling and Simulation pp. 79 — 112 Luniver Press

CoSMoS process, models and metamodels. Paul S. Andrews, Susan Stepney, Tim Hoverd, Fiona A. C. Polack, Adam T. Sampson and Jon Timmis. In Proceedings of the 2011 Workshop on Complex Systems Modelling and Simulation pp. 1 — 14 Luniver Press

Simulation validation: exploring the suitability of a simulation of cell division and differentiation in the prostate Fiona A. C. Polack, Alastair Droop, Philip Garnett, Teodor Ghetiu and Susan Stepney In Proceedings of the 2011 Workshop on Complex Systems Modelling and Simulation pp. 113 — 133 Luniver Press

Object Store Based Simulation Interworking Carl G. Ritson, Paul S. Andrews and Adam T. Sampson In Peter H. Welch, Adam T. Sampson, Jan B. Pedersen, Jon Kerridge, Jan F. Broenink and Frederick R.M. Barnes (eds.) Communicating Process Architectures 2011, volume 68 of Concurrent Systems Engineering pp. 243—254 IOS Press

The Best of Most Worlds: Shared Objects for Multilingual Simulation (PDF) Adam T. Sampson and Paul S. Andrews In 9th Workshop on Parallel/High-Performance Object-Oriented Scientific Computing (POOSC'10)

Using the CoSMoS Process to Enhance an Executable Model of Auxin Transport Canalisation (PDF) Philip Garnett, Susan Stepney, Francesca Day and Ottoline Leyser In Susan Stepney, Peter H. Welch, Paul S. Andrews and Adam T. Sampson (eds.) Proceedings of the 2010 Workshop on Complex Systems Modelling and Simulation pp. 9—32 Luniver Press

Arguing Validation of Simulations in Science (PDF) Fiona A. C. Polack In Susan Stepney, Peter H. Welch, Paul S. Andrews and Adam T. Sampson (eds.) Proceedings of the 2010 Workshop on Complex Systems Modelling and Simulation pp. 51—74 Luniver Press

Argument-Driven Validation of Computer Simulations — A Necessity Rather Than an Option (PDF) Teodor Ghetiu, Fiona A. C. Polack and James L. Bown In VALID 2010: The Second International Conference on Advances in System Testing and Validation Lifecycle pp. 1—4 IEEE Press

Formalising Harmony Seeking Rules of Morphogenesis (PDF) Tim Hoverd and Susan Stepney In Harold Fellermann, Mark Dörr, Martin M. Hanczyc, Lone Ladegaard Laursen, Sarah Maurer, Daniel Merkle, Pierre-Alain Monnard, Kasper Stoy and Steen Rasmussen (eds.) Artificial Life XII: Proceedings of the Twelfth International Conference on the Simulation and Synthesis of Living Systems pp. 386—393 MIT Press, Cambridge, MA

Exploiting loose horizontal coupling in evolutionary swarm robotics (PDF) Jennifer Owen, Susan Stepney, Jonathan Timmis and Alan F. T. Winfield In Proceedings of the 7th international conference on Swarm intelligence, ANTS'10 pp. 432—439 Springer-Verlag

Reflections on the Simulation of Complex Systems for Science (PDF) Fiona A. C. Polack, Paul S. Andrews, Teodor Ghetiu, Mark Read, Susan Stepney, Jon Timmis and Adam T. Sampson In ICECCS 2010: Fifteenth IEEE International Conference on Engineering of Complex Computer Systems pp. 276—285 IEEE Press

A Transactional Architecture for Simulation (PDF) Tim Hoverd and Adam T. Sampson In ICECCS 2010: Fifteenth IEEE International Conference on Engineering of Complex Computer Systems pp. 286—290 IEEE Press

A Domain Model of Experimental Autoimmune Encephalomyelitis (PDF) Mark Read, Paul S. Andrews, Jon Timmis and Vipin Kumar In Susan Stepney, Peter H. Welch, Paul S. Andrews and Jon Timmis (eds.) Proceedings of the 2009 Workshop on Complex Systems Modelling and Simulation, York, UK, August 2009 pp. 9—44 Luniver Press

Using UML to Model EAE and its Regulatory Network (PDF) Mark Read, Paul S. Andrews, Jon Timmis and Vipin Kumar In 8th International Conference on Artificial Immune Systems (ICARIS), volume 5666 of Lecture Notes in Computer Science

Environment Orientation: An Architecture for Simulating Complex Systems (PDF) Tim Hoverd and Susan Stepney In Susan Stepney, Peter H. Welch, Paul S. Andrews and Jon Timmis (eds.) Proceedings of the 2009 Workshop on Complex Systems Modelling and Simulation, York, UK, August 2009 pp. 67—82 Luniver Press

Equivalence Arguments for Complex Systems Simulations — A Case-Study (PDF) Teodor Ghetiu, Robert D. Alexander, Paul S. Andrews, Fiona A. C. Polack and James Bown In Susan Stepney, Peter H. Welch, Paul S. Andrews and Jon Timmis (eds.) Complex Systems Simulation and Modelling Workshop (CoSMoS 2009) pp. 101—140 Luniver Press

Multicore Scheduling for Lightweight Communicating Processes (PDF) Carl G. Ritson, Adam T. Sampson and Frederick R. M. Barnes In John Field and Vasco Thudichum Vasconcelos (eds.) Coordination Models and Languages, 11th International Conference, COORDINATION 2009, Lisboa, Portugal, June 9-12, 2009. Proceedings, volume 5521 of Lecture Notes in Computer Science pp. 163—183 Springer

Modelling and Simulation of Granuloma Formation in Visceral Leishmaniasis (PDF) Anton Jakob Flügge, Jon Timmis, Paul Andrews, John Moore and Paul Kaye In 2009 IEEE Congress on Evolutionary Computation (CEC 2009) pp. 3052—3059 IEEE Press

The engineering of concurrent simulations of complex systems (PDF) Fiona A.C. Polack, Paul S. Andrews and Adam T. Sampson In 2009 IEEE Congress on Evolutionary Computation (CEC 2009) pp. 217—224 IEEE Press

Mobile Processes, Mobile Channels and Dynamic Systems (PDF) Eric Bonnici and Peter H. Welch In 2009 IEEE Congress on Evolutionary Computation (CEC 2009) pp. 232—239 IEEE Press

Birds on the Wall: Distributing a Process-Oriented Simulation (PDF) Adam T. Sampson, John Markus Bjørndalen and Paul S. Andrews In 2009 IEEE Congress on Evolutionary Computation (CEC 2009) pp. 225—231 IEEE Press

Process-Oriented Collective Operations (PDF) John Markus Bjørndalen and Adam T. Sampson In Peter H. Welch, Susan Stepney, Fiona A.C. Polack, Frederick R.M. Barnes, Alistair A. McEwan, Gardner S. Stiles, Jan F. Broenink and Adam T. Sampson (eds.) Communicating Process Architectures 2008, volume 66 of Concurrent Systems Engineering pp. 309—328 IOS Press

Simulating biology: towards understanding what the simulation shows (PDF) Paul S. Andrews, Fiona Polack, Adam T. Sampson, Jon Timmis, Lisa Scott and Mark Coles In Susan Stepney, Fiona Polack and Peter Welch (eds.) Proceedings of the 2008 Workshop on Complex Systems Modelling and Simulation, York, UK, September 2008 pp. 93—123 Luniver Press

Complex systems models: engineering simulations (PDF) Fiona A.C. Polack, Tim Hoverd, Adam T. Sampson, Susan Stepney and Jon Timmis In S. Bullock, J. Noble, R. Watson and M. A. Bedau (eds.) Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems pp. 482—489 MIT Press, Cambridge, MA

Investigating patterns for the process-oriented modelling and simulation of space in complex systems (PDF) Paul S. Andrews, Adam T. Sampson, John Markus Bjørndalen, Susan Stepney, Jon Timmis, Douglas N. Warren and Peter H. Welch In S. Bullock, J. Noble, R. Watson and M. A. Bedau (eds.) Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems pp. 17—24 MIT Press, Cambridge, MA

Journal Publications

Spartan: A Comprehensive Tool for Understanding Uncertainlty in Simulations of Biological Systems, K. Alden, M. Read, J. Timmis, P. Andrews, H. Veiga-Fernades and M. Coles, PLoS Computational Biology, 2013.

Engineering simulations for cancer systems biology, Bown J, Andrews PS, Deeni Y, Goltsov A, Idowu M, Polack FA, Sampson AT, Shovman M, Stepney S, Current Drug Targets, 13(12):1560-74, 2012.

Differential RET signaling responses orchestrate lymphoid and nervous enteric system development. A. Patel et al.. Science Signalling. Vol 5, Issue 235, 2012.

Techniques for Grounding Agent-Based Simulations in the Real Domain: a case study in Experimental Autoimmune Encephalomyelitis M. Read, P. Andrews, J. Timmis and V. Kumar. Mathematical and Computer Modelling of Dynamical Systems (MCMDS), 18(1):67-86, 2012.

On artificial immune systems and swarm intelligence (PDF) Jon Timmis, Paul S. Andrews and Emma Hart In Swarm Intelligence, volume 4 number 4 pp. 247—273

Modelling fungal colonies and communities: challenges and opportunities (PDF) Ruth E. Falconer, James L. Bown, Eilidh McAdam, Paco Perez-Reche, Adam T. Sampson, Jan van den Bulcke and Nia A. White In IMA Fungus, volume 1 number 2 pp. 155—159

Workshop Proceedings

Proceedings of the 2013 Workshop on Complex Systems Modelling and Simulation (PDF) Susan Stepney and Paul S. Andrews (eds.) Luniver Press

Proceedings of the 2012 Workshop on Complex Systems Modelling and Simulation (PDF) Susan Stepney, Paul S. Andrews and Mark N. Read (eds.) Luniver Press

Proceedings of the 2011 Workshop on Complex Systems Modelling and Simulation (PDF) Susan Stepney, Peter H. Welch, Paul S. Andrews and Carl G. Ritson (eds.) Luniver Press

Proceedings of the 2010 Workshop on Complex Systems Modelling and Simulation (PDF) Susan Stepney, Peter H. Welch, Paul S. Andrews and Adam T. Sampson (eds.) Luniver Press

Proceedings of the 2009 Workshop on Complex Systems Modelling and Simulation, York, UK, August 2009 (PDF) Susan Stepney, Peter H. Welch, Paul S. Andrews and Jon Timmis (eds.) Luniver Press

Proceedings of the 2008 Workshop on Complex Systems Modelling and Simulation, York, UK, September 2008 (PDF) Susan Stepney, Fiona Polack and Peter Welch (eds.) Luniver Press

Posters

Using Models in Complex Systems Simulation Paul Andrews, Fiona Polack, Adam Sampson, Susan Stepney and Jon Timmis In Epistemology of Modeling and Simulation 2011

Towards a Principled Design of Bio-inspired Solutions to Adaptive Information Filtering Nurulhuda Firdaus Mohd Azmi, Jon Timmis and Fiona Polack In ICECCS 2010: Fifteenth IEEE International Conference on Engineering of Complex Computer Systems pp. 315—316 IEEE Press

Towards Self-Healing Swarm Robotic Systems Inspired by Granuloma Formation Amelia Ritahani Ismail and Jon Timmis In ICECCS 2010: Fifteenth IEEE International Conference on Engineering of Complex Computer Systems pp. 313—314 IEEE Press

In Search of Sound ``in silico'' Research - Validating a Complex System Simulation Teodor Ghetiu, Fiona A. C. Polack and James L. Bown In ICECCS 2010: Fifteenth IEEE International Conference on Engineering of Complex Computer Systems p. 312 IEEE Press

Complex Systems Modelling and Simulation Infrastructure Susan Stepney and Peter H. Welch In European Conference on Complex Systems 2009

Arguing the Validity of Models and Simulations for Scientific Exploration Fiona A. C. Polack, Paul S. Andrews, Teodor Ghetiu and Robert D. Alexander In European Conference on Complex Systems 2009

CoSMoS scale simulations and the path towards scientific validation (PDF) Teodor Ghetiu, Fiona A. C. Polack and James L. Bown In BES Symposium 2009: Facilitation in Plant Communities

Project Documents

The CoSMoS Process Version 0.1: A Process for the Modelling and Simulation of Complex Systems (PDF) Paul S. Andrews, Fiona A. C. Polack, Adam T. Sampson, Susan Stepney and Jon Timmis Department of Computer Science, University of York Number YCS-2010-453

Generative Patterns of Software (PDF) Tim Hoverd Qualifying dissertation

Modelling for the Faint-Hearted (PDF) Tim Hoverd Tutorial given at ICARIS 2009.

Related Papers

Concurrency, Intuition and Formal Verification: Yes, We Can! (PDF) Jan B. Pedersen and Peter H. Welch In 2010 Workshop on Curricula for Concurrency and Parallelism

Santa Claus: Formal analysis of a process-oriented solution Peter H. Welch and Jan B. Pedersen In ACM Transactions on Programming Languages and Systems, volume 32 number 4 pp. 1—37 ACM

Checking Process-Oriented Operating System Behaviour using CSP and Refinement Frederick R. M. Barnes and Carl G. Ritson In SIGOPS Operating Systems Review, volume 43 number 4 pp. 45—49 ACM

Alloy: Fast Generic Transformations for Haskell (PDF) Neil C.C. Brown and Adam T. Sampson In Haskell '09: Proceedings of the 2009 ACM SIGPLAN Haskell Symposium pp. 105—116

Two-Way Protocols for occam-pi (PDF) Adam T. Sampson In Peter H. Welch, Susan Stepney, Fiona A.C. Polack, Frederick R.M. Barnes, Alistair A. McEwan, Gardner S. Stiles, Jan F. Broenink and Adam T. Sampson (eds.) Communicating Process Architectures 2008, volume 66 of Concurrent Systems Engineering pp. 85—97 IOS Press

Matching and Modifying with Generics (PDF) Neil C.C. Brown and Adam T. Sampson In Trends in Functional Programming (TFP) 2008 pp. 304—318