Selected Publications
1. M. Calder, J. Hillston
Process algebra modelling styles for biomolecular processes.
Transactions on Computational Systems Biology XI, LNBI 5750, pp.1-25, Springer, 2009.
2. M. Calder, P. Gray and C. Unsworth
Tightly coupled verification of pervasive systems
Proceedings of the Third International Workshop on
Formal Methods for Interactive Systems (FMIS 2009) Electronic Communications of the EASST, volume X, 2009.
3. M. Calder, S. Gilmore, J. Hillston
and V. Vyshemirsky
Formal methods for biochemical signalling pathways
To appear in Formal Methods: State of the Art and New Directions, Springer, to
appear.
4. A.
Miller and M. Calder.
An automatic abstraction technique for verifying featured, parameterised
systems
Theoretical Computer Science, 404, pp. 235-255, 2008.
5. F.
Ciochetta, A. Degasperi, J. Hillston, M. Calder.
Some investigations concerning the CTMC and the ODE model derived from
Bio-PEPA
Proceedings of FBTC 2008, ENTCS vol. 17350, Elsevier, 2008.
6. M. Calder,
Computational Methods for Systems Biology
Theoretical Computer Science, volume 408,
Elsevier, 2008.
7. D. Graham, M. Calder, and A Miller
An Inductive Technique for Parameterised Model Checking of Degenerative
Distributed Randomised Protocols
Proceedings of AVOCS 07 (Automated Verification of Critical Systems), ENTCS
vol. 250, pp.87-103, Elsevier
2009.
8. M. Calder, S. Gilmore (Editors)
Computational Methods for Systems Biology Lecture Notes in Bioinformatics, volume 4695, Springer, 2007.
9. M. Calder, S. Gilmore and J.
Hillston
Modelling the influence of RKIP on the ERK signalling pathway using the
stochastic process algebra PEPA
Transactions on Computational Systems Biology VII, vol. 4230, pp. 1-23,
Springer, 2006.
10. A. Miller, A. Donaldson and M.
Calder
Symmetry in temporal logic model checking
Computing Surveys, ACM ,vol. 38, issue 3,pp. 1-36, 2006.
11. A. Miller, M. Calder and A.
Donaldson
A template-based approach for the generation of abstractable and reducible
models of featured networks
Computer Networks, vol.
51(2), pp. 439-455, Elsevier, 2007.
12. M. Calder, A. Duguid, S. Gilmore and
J. Hillston.
Stronger computational modelling of signalling pathways using both continuous
and discrete-space methods
Computational Methods in Systems Biology (CMSB 2006), LNBI vol. 421, pp.
63-78, 2006.
13. M. Calder, V. Vyshemirsky, D.
Gilbert, and R. Orton.
Analysis of Signalling Pathways using Continuous Time Markov Chains
Transactions on Computational Systems Biology VI, vol. 4220, pp. 44-67,
Springer, 2006.
14. M. Calder and A. Miller
Feature
Interaction Detection by Pairwise Analysis of LTL Properties--a case study
Formal Methods in System Design, Volume 28(30), pp. 213-261, May 2006.
15. M. Calder and J. Hillston
What do scaffold proteins really do?
Fifth Workshop on Process Algebra and Stochastically Timed Activities
(PASTA 2006),
16. A.
Miller and M. Calder.
A generic approach for the automatic verification of featured, parameterised
systems
Proceedings of Eighth International Conference on Feature Interactions in
Telecommunications and Software Systems (ICFI '05) , pp 217-235, IOS Press, 2005.
17. M. Calder, S. Gilmore and J.
Hillston.
Automatically deriving ODEs from process algebra models of signalling pathways
Proceedings of CMSB 2005 (Computational Methods in Systems Biology), pp 204-215, 2005.
18. M. Calder, V. Vyshemirsky, D. Gilbert
and R. Orton.
Analysis of Signalling Pathways using the Prism Model Checker
Proceedings of CMSB 2005 (Computational Methods in Systems Biology), pp 179-190, 2005.
19. W. Kolch, M. Calder and D. Gilbert.
When kinases meet mathematics: the systems biology of MAPK signalling
FEBS Letters, vol. 579, pp 1891--1895, 2005.
20. R. Orton, O. Sturm, V. Vyshemirsky, M. Calder,
D. Gilbert and W. Kolch.
Computational Modelling of the Receptor Tyrosine Kinase Activated MAPK
Pathway
Biochemical Journal, vol. 392, pp 249--261, 2005.
21. M. Calder, S. Gilmore and J. Hillston.
Modelling the influence of RKIP on the ERK signalling pathway using the
stochastic process algebra PEPA
Proceedings of Bio-CONCUR 2004, Electronic Notes in Theoretical Computer Science,
2004.
22. A. Donaldson, A. Miller and M.
Calder.
Finding symmetry in models of concurrent systems by static channel diagram
analysis
Electronic Notes in Theoretical Computer Science, vol. 128/6, pp 161-177,
Elsevier, 2004.
23.
M
Calder and A. Miller.
Verifying
parameterised, featured networks by abstraction
Proceedings of the first
International Symposium on Leveraging Applications of Formal Methods (ISOLA'04), pp 227--234.
24.
M Calder and A. Miller.
Detecting
Feature Interactions: how many components do we need?
Objects, Agents and Features. Lecture Notes in Computing Science, vol.
2975, pp 45-66, 2004.
25. P.Saffrey and M. Calder.
Optimising
Communications Structure for Model Checking Lecture Notes in Computer Science,
Proceedings of FASE 2004, Lecture Notes in Computer Science, vol. 2984,
pp 310-3224, Springer Verlag, 2004.
26.
A.Miller
and M Calder.
An
application of abstraction and induction techniques to degenerating systems of
processes.
Proceedings of the International Workshop on Model-Checking for
Dependable Software Intensive Systems (MCDSIS '03), IEEE Computer Society
Press, 2003.
27.
M
Calder, M. Kolberg E. Magill, D. Marples and S. Reiff-Marganiec.
Hybrid Solutions
to the Feature Interaction Problem
Feature Interactions in Telecommunications and Software Systems VII, IOS
Press. pp.187-205, 2003.
28.
M Calder and A. Miller
Generalising
Feature Interactions in Email
Feature Interactions in Telecommunications and Software Systems VII,
IOS Press. pp. 295-217, 2003.
29.
M
Calder, E. Magill, M. Kolberg, and S. Reiff-Marganiec.
Feature
Interaction: A Critical Review and Considered Forecast.
Computer Networks, Volume
41/1, pp. 115-141, North-Holland. January 2003.
30.
M.
Calder and A. Miller.
Using SPIN to
Analyse the FireWire Protocol -- a Case Study.
Formal Aspects of Computer Science, vol. 14, no. 3, pp. 247266, Springer
Verlag, 2003.
31.
M. Calder and A. Miller.
Automated
verification of any number of concurrent, communicating processes.
Proceedings of 17th IEEE Automated Software Engineering (ASE 2002),
pp. 227-230, IEEE, 2002.
32.
M. Calder and A. Miller.
Five
ways to use symmetry and induction in the verification of networks of processes
using model-checking.
Proceedings of Automated Verification of Critical Systems (AVoCS),2002.
33. M.
Calder, S. Maharaj, and C. Shankland.
A Modal Logic for
Full LOTOS based on Symbolic Transition Systems.
The Computer Journal, Volume 45, No.1, pp. 55--61, 2002.
34.
M. Calder and A. Miller.
Using
SPIN for Feature Interaction: Analysis -- a Case Study.
Proceedings of the 8th International SPIN Workshop (SPIN 2001), Toronto,
Canada, Lecture Notes in Computer Science, Volume 2057, pp. 143--162,
2001.
35.
M. Calder and A. Miller.
Using
the Model Checker SPIN to Detect Feature Interactions in Telecommunications
Services.
36.
M. Calder, S. Maharaj, and C. Shankland.
An
Adequate Logic for Full LOTOS.
Proceedings of FME 2001, Lecture Notes in Computer Science. vol.
2021, pp.384-395, 2001.
37.
M. Calder and C. Shankland.
A Symbolic
Semantics and Bisimulation for Full LOTOS.
Proceedings of FORTE 2001, 21st International Conference on Formal
Techniques for Networked and Distributed Systems,
38.
M Calder, E. Magill, S. Reiff-Marganiec, and V.
Thayananthan.
Theory
and Practice of Enhancing a Legacy Software System.
To appear in Systems Engineering for Business Process Change (volume 2),
P.Henderson (ed.) Springer-Verlag, 2001.
39.
M. Calder and S. Reiff.
Modelling
Legacy Telecommunications Switching Systems for Interaction Analysis.
Systems Engineering for Business Process Change, P. Henderson (ed.), pp.
182-195, Springer-Verlag, 2000.
40.
M. Calder and
Feature Interactions in Telecommunications and Software Systems VI.
IOS Press, 2000.
41.
M. Calder, E. Magill and D. Marples.
A Hybrid
Approach to Software Interworking Problems: Managing Interactions between
Legacy and Evolving Telecommunications Software.
IEE Proceedings - Software, Vol. 146, No. 3, June 1999.
Abstract only in electronic form, please contact the authors for a hard copy of
the full paper.
42.
M. Calder and C. Shankland.
A Symbolic
Semantics and Bisimulation for Full LOTOS.
43. M.
Calder.
What Use are
Formal Analysis and Design Methods to Telecommunications Services?
In Feature Interactions in Telecommunications and Software Systems, pp.
23-31, IOS Press, 1998.
44.
M. Thomas.
Modelling and
Analysing User Views of Telecommunications Services.
In Feature Interactions in Telecommunications Systems, pp.
168-183, IOS Press, 1997.
45.
P. Jeffcutt and M. Thomas.
Organisation,
Information and Computation.
ORGANIZATION, 5/3, pp. 397-423, August 1998.
46.
M. Calder and A. Miller.
Analysing a Basic
Call Protocol using PROMELA/XSPIN.
Proceedings SPIN '98: Workshop on Automata Theoretic Verification with
the SPIN model Checker, pp. 169-181,
47.
C. Shankland and M. Thomas.
Symbolic
Bisimulations for Full LOTOS.
In Lecture Notes in Computer Science vol. 1349, pp. 479-493,
Springer-Verlag, 1997.
48.
S. Aitken, P. Gray, T. Melham, and M. Thomas.
A Study of User
Activity in Interactive Theorem Proving.
Journal of Symbolic Computation, vol. 25, no. 2, pp. 263-284,
February 1998.
49. M.
Thomas.
Formal Methods and
their Role in Developing Safe Systems.
High Integrity Systems Journal, Volume 1, Number 5, Oxford
University Press, pp. 447-451, 1996.
50. C. Kirkwood and M. Thomas.
Experiences
with LOTOS: A Report on Two Case Studies.
Proceedings of WIFT '95 159-172, pp. IEEE Computer Society Press,
1995.
51. M. Thomas
and B. Ormsby.
On the Design of
Side-Stick Controllers in Fly-By-Wire Aircraft.
ACM Applied Computing Review , Volume 2, Number 1, Spring 1994.
(Sometimes the picture causes ghostview problems; a version of the paper without
the graphic is here.)
52. U. Martin
and M. Thomas.
Verification Techniques
for LOTOS.
Proceedings of Formal Methods
53.
M. Thomas.
The Story of the
Therac-25 in LOTOS.
High Integrity Systems Journal, Volume 1, Number 1, Oxford University
Press, pp. 3-17, 1994.
54. M.
Thomas.
A Proof of
Incorrectness using LP: the Editing Problem from the Therac-25.
High Integrity Systems Journal, Volume 1, Number 1, Oxford
University Press, pp. 35-49, 1994.
61. M. Thomas and K. Jantke
Inductive
Inference for Knuth Bendix Completion
Lecture Notes in Computer Science vol. 397 288-303, Springer
Verlag, 1989.