Publications in 2009

• Submitted 2009 James T. Murphy and Ray Walshe, "Modelling Antibiotic Resistance in Bacterial Colonies Using Agent-Based Approach" as Chapter 8 of "Understanding the Dynamics of Biological Systems:Lessons Learned from Integrative Systems Biology" edited by Prof Werner Dubitsky (UU) Springer Verlag Publishers
• Submitted 2009 "A Theoretical Analysis of the Pro-Drug Delivery System for Treating Antibiotic-Resistant Bacteria" by James T. Murphy, Ray Walshe, and Marc Devocelle to IEEE/ACM Transactions-in Computational Biology and Bioinformatics"
• Murphy J.T., Walshe R. and Devocelle M., 2009 "Modelling the Population Dynamics of Antibiotic-Resistant Bacteria: An Agent-Based Approach", International Journal of Modern Physics C, 20(3):435-457

Publications in 2008

• Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md. Mehedi Hasan, Mohammad Shoyaib, Haseena Khan and Ray Walshe, "Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach", BMC Bioinformatics, 2008, 9:414., 2008
• Murphy J.T., Walshe R. and Devocelle M., 2008 "A Computational Model of Antibiotic-Resistance Mechanisms in Methicillin-Resistant Staphylococcus aureus (MRSA)", Journal of Theoretical Biology, 254(2):284-93.
• Murphy J.T., Walshe R. and Devocelle M., 2008 "High Performance Computing for Modelling Bacterial Communities", ERCIM News No. 74:37-38.
• Perrin, D., Ruskin, H. J., Crane, M., and Walshe, R. (2008). Epigenetic modelling. ERCIM News, 72:46.
• Murphy J.T., Walshe R. and Devocelle M., 2008 "An Agent Based Approach to Modelling Microbial Ecosystems", ERCIM News No. 73:39-40.
• Murphy J.T., Walshe R. and Devocelle M., 2008 "A Novel Cellular Model of Methicillin-Resistant S. aureus (MRSA) for Predicting Antibiotic Susceptibility", Genomes 2008 - Functional Genomics of Microorganisms conference, April 8-11 2008, Institut Pasteur, Paris, France.
• Alessandro Curioni and Ray Walshe. (2008) Introduction to the Special Theme: Supercomputing at Work, ERCIM News No. 74, July 2008 pp 14-15.

Publications in 2007

• R.J. Walshe, H. J. Ruskin and A. Callaghan (2008) "Multi-Agent Simulations of the Immune Response to HIV During the Acute Stage of Infection" International Journal of Modern Physics C, Volume 19, Issue 01, pp. 15-32 (2008).
• James T. Murphy, Ray Walshe and Marc Devocelle (2007) "Agent-Based Model of Methicillin-Resistant Staphylococcus aureus and Antibiotics in Batch Culture" Accepted for Publication in Proceedings of ESM2007 The 21st European Simulation and Modelling Conference,St.Julian's, Malta

Publications in 2006

• Ashley Callaghan, Heather J. Ruskin, Ray Walshe (2006) "Analysis of the relative importance of the humoral versus the cellular response during the acute stage of HIV infection: Results from multi-agent computer simulations." In Proceedings of the 20th Annual European Simulation and Modelling Conference, Edited by Alexandre Nketsa, Mario Paludetto and Cyrille Bertelle, Eurosi-ETI, pp.271-276 ISBN 90-77381-30-9
• Murphy J.T. and Walshe R., (2006). "Micro-Gen: An Agent-Based Model of Bacteria-Antibiotic Interactions in Batch Culture", in proceedings of the 20th Annual European Simulation and Modelling Conference,Edited by Alexandre Nketsa, Mario Paludetto and Cyrille Bertelle, Eurosi-ETI, pp. 239-242.
• Walshe, Ray (2006) Modelling Bacterial Growth Patterns in the presence of Antibiotic, In the Proceedings of 11th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS 2006), IEEE Computer Society, pp 177-186
• O'Leary C., Humphrys M. and Walshe R. (2006). Collaborative Online Development of Modular Intelligent Agents, ERCIM News No. 64, pp 30-31
• Ruskin H. and Walshe R. (2006). Introduction to the Special Theme: Emergent Computing, ERCIM News No. 64, January 2006 pp 24-25.

Publications in 2005

• O'Leary, C.; Humphrys, M.; Walshe, R . (2005) A novel application of Web Services in Computer Science education, In: Proceedings of The IEEE International Conference on Computer as a Tool, (EUROCON 2005) Volume: 1, IEEE , pp 807- 810
• Grainne Kerr, Ray Walshe, Marian Duggan, Chris Pender and Ronan Winters.(2005) Bacteria-Antibiotic Interaction Tool:ALIFE Simulation, BioINFROM 2005, Dublin CIty Univesity.
• Kerr G., Walshe, R. (2005). BAIT: Bacteria - Antibiotic Interaction Tool, ERCIM News No. 60, January 2005.

Publications in 2004

• O'Leary, C., Humphrys, M. and Walshe, R., (2004) Constructing an animat mind using 505 sub-minds from 234 different authors,Proceedings of the Eighth International Conference on the Simulation of Adaptive Behavior, From Animals to Animats 8 (SAB 2004), S. Schaal, A.J. Ijspeert, A. Billard, S. Vijayakumar, J. Hallam, and J.-A. Meyer (Eds.), Pg 39-49, MIT Press, Cambridge, ISBN 0-262-69341-0, 2004
• Walshe, R., Humphrys, M. and O'Leary, C. (2004) Constructing Complex Brains: Building minds using sub-minds from biotechnology authors in Proceeding of The Symposium on Professional Practice in AI, E. Mercier-Laurent, J. Debenham (Eds.), ISBN:2-907801-05-8, IFIP Press 2004
• Kerr, G., (w. R. Walshe, M. Duggan, C. Pender, R. Winters), (2004) at Annual BioNet Conference, Institute of Technology Carlow, The BAIT Simulation: Bacteria Antibiotic Interaction Tool.

Publications in 2002

• Walshe, R. (2002). Online Virtual Tutorials: Increasing Access to Peer to Peer Tutoring. In G. Richards (Ed.), Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2002 (pp. 2349-2352). Chesapeake, VA: AACE.
• Charlie Daly, Dave Donnellan, Monica Ward and Ray Walshe (2002), The Lab Tutor System of a Large Undergraduate Class: the Lab Tutor's perspective: Staff & Educational Development Association & All Ireland Society for Higher Education Joint Conference, Dublin
• Walshe, Ray (2002) Online Virtual Tutorials using Discussion Forums: A Mechanism to Aid Peer-to-Peer Tutoring,In: Proceedings of the 16th International Conference on Systems for Automation of Engineering and Research (SAER 2002), Bulgaria, pp.. ISBN: 954-8329-42-5

Publications in 2001

• Walshe, R., (2001) The Origin of the Speeches: language evolution through collaborative reinforcement learning, in Proceedings of Intelligent Virtual Agents, Third International Workshop, IVA 2001, A. de Antonio, R. Aylett D. Ballin (Eds.), LNCS 2190, ISBN 3-540-42570-5, Springer
• Ray Walshe, Mark Humphrys (2001) First Implementation of the World-Wide-Mind.in Proceedings of 6th European Conference on Artificial Life, ECAL 2001, :Jozef Kelemen and Petr Sos (Eds.),LNCS 2159, ISBN 3-540-42567-5,Springer-Verlag, pp 714-718

Publications in 2000

• Ray Walshe, Margaret Farren, Ray O'Neill (2000): Setanta: a school based intranet project, in Proceedings of World Conference on the WWW and Internet, WebNet 2000, Gordon Davies and Charles B. Owen, (Eds), ISBN 1-880094-40-1, AACE, pp 975-976
• Farren, M. Walshe, R., O'Neill, R , (2000) Collaborative ICT Project to improve teaching and learning. Seventh International Conference, Integrating Learning Technology: Practice, Policy and Partnership. UMIST, Manchester, UK September 2000

Talks

• Ruskin, H.J., Crane, M., Walshe, R., June 7th 2005. "Biocomputation at DCU", Albert Einstein Medical College, NY, USA.

Masters Students

• An Examination of the use of a Typing Tutorial Package to benefit Word Processing in a Senior Primary Class::Joseph Carty, 1999
• A Study of the Relationship between Computer Usage and Self-Esteem::Mary Quinn 2000
• A Comparison of Teaching Geography In the Primary School using the Internet and a Conventional Approach:: Christine Flanagan 2001
• BAIT - Bacteria Antibiotic Interaction Tool:An Artificial Life Simulation Tool :: Ronan Winters, Marian Duggan, Gráinne Kerr and Christopher Pender 2004
• Genetic Regulatory Network for mRNA expression Data:: Trevor Logue and Venkata Jitendra Gopisetty 2005
• Using Prior Knowledge and Genetic Algorithm in the Elucidation of Genetic Regulatory Networks from mRNA Microarray data :: Melanie Rycraft and Neil Byrne 2006
• Agent–Based Simulation of Eutrophication Model in Lake :: Maja Julardžija and Yao Yao 2007

PhD Students

• James T. Murphy (2008)

Program Committees

• SCI2003 7th World Multconference on Systems,Cybernetics and Informatics , Orlando, Florida USA,July 27th-30th 2003
• Artificial Intelligence and Cognitive Science (AICS) since 2000
• Evolutionary Biology (EvoBIO) since 2006
• The Genetic and Evolutionary Computation Conference (GECCO) since 2006
• The 2nd International Conference on Natural Computation 2006
• The 3rd International Conference on Fuzzy Systems and Knowledge Discovery 2006
• International Conference on the Principles and Practice of Programming in Java 2002-2004
  

  Session Chairs

  • World Conference on E-Learning in Corporate, Government, Healthcare and Higher Education E-Learn 2002 -- Montreal, Canada Oct. 15-19, 2002
  
  

  Journal Reviewer

  • International journal on Systemics, Cybernetics and Informatics (SC&I)

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