/ +44 1904 325337
- Senior Lecturer, YCCSA / Department of Computer Science, University of York
- Head of College, Langwith College, University of York
- Fellow, Higher Education Academy.
Enterprise Systems and
Non-standard Computing research groups, Department of Computer Science, York.
Member of YCIL, the York Computational Immunology Lab
Member of YCCSA, the York Centre for Complex Systems Analysis, an interdisciplinary research group.
Member of the Biological Physical Sciences Institute (BPSI), University of York
Recent publications -- CV: pdf.
Supporting computer simulation as a research tool
I work in software engineering, model driven engineering, and the use of these in development and use of demonstrably fit-for-purpose complex systems simulations for use in scientific research.
Imagine trying to solve a problem such as the origin of cancer
without being able to observe what the cells are doing,
or how they are affected by treatment. That is essentially the situation
that we are currently in. Most studies of biologically-complex systems are
based on counting cells and analysing chemical properties.
A computer simulation can mimic behaviour, as well as being able to provide
data such as cell counts. A computer simulator can be changed to try out new
hypotheses much more easily than a laboratory analysis. However, we need robust,
understandable ways to develop fit-for-purpose computer simulations, and to collaborate
with the scientists who can use computer simulation to complement their traditional
PhD topics: I am interested in applications for doctoral study in aspects of model
driven engineering for non-OO models (state charts, Petri nets,
activity diagrams, etc.) and for process-oriented target languages. In addition, the wider software engineering of complex simulations is of interest, including testing, fitness-for-purpose, reuse and maintenance of complex simulations.
See here for some potential PhD projects which cover the following areas:
- Engineering nature-inspired and complex systems
- Simulating complex scientific systems
- Modelling, simulation, and validation of complex systems
- Modelling and metamodelling
- Model-driven software engineering, particularly in non-OO contexts
MSc by Research: 2015-16: interdisciplinary simulation project
Collaborations and Grants
Wellcome/C2D2 Consolidator grant for YCIL (PI Jon Timmis): Electronics, CII/Biology, Computer Science: January-December 2014.
EPSRC Impact Accelerator: UoY preliminary study grant: a collaborative initiative in graphene modelling: Physics, Electronics and Computer Science.
Summer school studentship, prostate cell simulation: with Norman Maitland (Biology cancer lab), Susan Stepney (YCCSA/CS).
Funded by Wellcome C2D2 (internal) grant: July to October 2012. The summer project will implement the
cell simulator for cancer and BPH. The grant also pays for materials for use by an intern in
Biology who will provide data for the simulation.
Sounds Different: a feasibility study of flexible load balancing in sound sensor networks: with
Leandro Soares indrusiak (CS Real Time Systems), Dave Chesmore (Electronics Audio Lab), Paul Mitchell (Electronics Wireless sensor networks)
Load balancing: using bio-inspired algorithms in simulation and reality. Funded by University of York: May to July 2012.
CoSMoS (Complex systems modelling and simulation infrastructure), led by Prof. Stepney (PI York), York, Prof. Peter Welch
(PI Kent), with co-investigators Dr
Fred barnes (Computer Science, Kent), Prof. Andy Tyrrell (Electronics,
York), Prof. Jon Timmis (Computer Science and Electronic, York) and Prof. Christopher Alexander
(architecture); and collaborators Dr Jim Bown (Abertay) and Prof. Alan
Winfield (UWE). EPSRC grants EP/E053505/1 and EP/E049419/1, 2007-10, supporting capacity building in
modelling and simulation techniques for complex systems.
TUNA (Theory Underpinning Nanite Assemblers), in collaboration with
Prof. P. Welch, Kent; Prof. S. Schneider and Dr. H. Treharne, Surrey;
Profs. Stepney (PI) and Woodcock and Dr Cavalcanti, York. EPSRC grant EP/C516966/1, 2004-5, supporting a feasibility study on the
engineering of emergent systems.
Rigorous information systems development, in collaboration with Prof. R. Laleau, Paris-12 Fontainebleau et IIE-CNAM, Paris (UML extensions, formality):
EPSRC grant 006R02664, 2003-6, supporting the Prof. Laleau as a visiting researcher (3 months over 3
International Conference on Unconventional Computation 2006, with
Susan Stepney (PI) and Jon Timmis:
EPSRC grant EP/D076420/1: costs related to running of conference,
particularly of invited speakers. March 06 to Feb 07.
Summer internship projects
Identifying characteristics of flocks, using statistics and information theory (T. Pinto, 2011): CS/Maths: YCCSA funded
Prostate cell simulation (A. Simeonescu, 2012): CS/Biology (N. Maitland): Wellcome C2D2 funded
Prostate cell simulation (L. Dia, 2013): CS/Biology (N. Maitland): YCCSA funded
Graphene modelling (D. Shearer, 2013): Physics (Y. Hancock)/CS/Electronics: EPSRC/University funded
Modelling bladder epithelium (F. Kazazi, 2015): CS/Biology (J. Southgate): YCCSA funded
Research Degrees Supervised
- Thitima (Jill) Srivatanakul, Methods for security, 2001-04 (with
Prof. J. A. Clark) PhD awarded September 2005.
- Nuno Amalio, Formal software engineering, (with S. Stepney),
PhD awarded February 2007.
- Dimitrios Kolovos, Model consistency and composition, 2005-07 (with
R. F. Paige)), PhD awarded December 2008.
- Xiaocheng Ge, Engineering secure databases, 2002-07 (with
R. F. Paige), PhD awarded December 2008.
- Louis Rose, Model driven engineering, 2007-10 (with R. F. Paige),
PhD awarded 2011.
- Andrew Weeks, Non-standard computation, 2005-8 (with S. Stepney):
submitted March 2010: PhD awarded 2012.
- Malihe Tabatabaie, 2007-10 (with R. F. Paige): PhD awarded 2012
- James Williams, 2009-13 (with R. F. Paige): PhD awarded 2013
- Nurulhuda Mohd Azmi, artificial immune systems 2008-11 (with
J. Timmis), PhD awarded 2014
- Teodor Ghetiu, Modelling and simulation (CoSMoS project), 2008-11
(with Dr Jim Bown, Abertay), PhD awarded 2015.
- Asmiza Abdul Sani, model driven approaches and formal methods (with
R. Paige), PhD awarded 2015.
- Paul Taylor, autonomous adaptation of business processes (EngD,
BT sponsored) 2011-15 (with J. Timmis) Awarded January 2016.
Current Research Supervision
- Yujie Chen, vehicle routing (EngD, Gaist sponsored) 2013-16 (with Peter Cowling)
- Philip Mourdjis, delivery scheduling (EngD) 2013-16 (with Peter Cowling)
- Aastha Kakaria, agent models of traffic (MSc) 2015-16
- Alfa Yohannis, gamification design framework (PhD) 2016-19 (with Dimitris Kolovos)
Other Research Matters
- Chair, CoSMoS Special Session, ICECCS Conference, 2010
- Member, Programme Committee, ICARIS Conference, 2010
- Member, Programme Committee, ICARIS Conference, 2009
- Member, Programme Committee, CEC Conference, 2009
- Member, Programme Committee, CPA Conference, 2008
- Member, Programme Committee, SPC Security in Pervasive Computing
- Member, Progamme Committee, International Conference of Z and B users
(formally Z User Meeting), 2000-2005
- Member, Progamme Committee, ICFEM International Conference
on Formal Engineering Methods, 2005
- IIE-CNAM Chercheur invitee, 1999 and 2001
Recent past modules:
I have also taught Pascal programming,
various systems analysis, software engineering and database modules, to
MScs and to second year undergraduates. I developed and led teaching associated with ISM projects
for third year students.
External Examiner, Research Degrees
- External PhD Examiner, I. Wood, Teesside, UK, 2003 (Pass)
- External MSc Examiner, G. Ravalli, Swinburne, Australia,
- External PhD Examiner, Chien-An Chen, Open, UK, 2007 (Pass)
- External PhD Examiner, Martin Robbins, Aberystwyth, 2009
- External PhD Examiner, Gavin Smith, University of South
- External PhD Examiner, D. Warren, Kent, UK (2012: ongoing)
- External PhD Examiner, C. Chibaya, Rhodes, S. A, 2013 (pass)
Internal Examiner, Research Degrees
- Internal MSc Assessor: Yang Liu, 2003-4 (Pass).
- Internal MSc Assessor: Hong (Alex) Lin, 2003-4 (Pass).
- Internal MSc Assessor: Angela Freitas, 2004-5 (Distinction).
- Internal PhD Assessor: Raman Ramsin, 2003-5 (Pass).
- Internal PhD Assessor: Mohd Syazwan Abdullah, 2003-5 (Pass).
- Internal PhD Assessor: Kester Clegg, 2005-8 (Pass).
- Internal PhD Assessor: Paul Andrews, 2005-8 (Pass).
- Internal PhD Assessor: Nicholas Drivalos Matragkas, 2006-11 (pass).
- Internal MSc Assessor: Richard Greaves, 2010-11 (Distinction recommended).
- Internal PhD Assessor: : A. Ritahani Ismail, 2008-2011 (Pass).
- Internal PhD Assessor: Linling Sun, 2008-11 (pass).
- Internal PhD Assessor: Daniel Mayo, 2010-13 (Pass).
- Internal PhD Assessor: Masoumeh Taromirad, 2011-14 (Pass).
Thesis Advisory Panel, Research Degrees
- Internal PhD Assessor: Xiaohu Liu (Electronics), 2010-13 (referred 2015).
- Internal PhD Assessor: Rafidah Pakir Mohamad, 2011-15 (submitted 2015).
- Internal PhD Assessor: Alan Millard, 2011-15.
- Internal PhD Assessor: Hao Wei, 2013-16
- Internal EngD Assessor: Rob Palin, 2013-17
- Internal PhD Assessor: Sophie Alexander, 2013-17
- Internal PhD Assessor: Peter Buckley (Electronics: CII), 2015-2018
- Internal MSc Assessor: Saheed Popoola, 2015-16
- PhD TAP member: Johnny German Leonov (Biology) 2012-15 (PhD awarded 2015)
Degree Course External Examiner
- External Examiner, BSc in Software Engineering, Westminster,
- External Examiner, MSc in Information Systems, TASMAC India/University of Wales,
2008-termination of franchise, March 2010
- External Examiner, MSc in Computer Science, Aberystwyth,
- External Examiner, University of Wales BSc in Computer Science,
franchised to A. de Nebrija, Madrid, 1998-2003
- Head of College, Langwith College (20% FTE).
- Science Faculty Appeals Chair and Member, University Special Cases Committee
- Chair, Departmental Research Studies Committee
- MSc SWE: admissions tutor
- Elected member, University Senate
Selected Past Administrative responsibilities
- Departmental lead, undergraduate and postraduate modular revision of all
taught degrees, 2007-10.
- Programme Lead, MSc in Sofware Engineering, 2012-2015
- Chair, Board
of Studies in Computer Science 2001-2004
- Co-ordinator for postgraduates who teach, Department of Computer
- Deputy Chair, University Special Cases Committee (2013)
- Member, University Promotions Committee (2010-11)
- Elected member, University Senate (to 2009)
- Member, University Promotions Committee: teaching sub-committee (2009-10)
- Member, University Court (to 2009)
- Member, University Student Skills Implementation Group (to 2009)
- Member, University Senate Review Group (to 2009)
- University Harrassment Adviser (to 2013)
(first-contacts for staff and students who think that they may be
victims of harrassment).