Biocomputation Research Lab - Dublin City University, Ireland

Publications , Presentations and Current Submissions

Recent Publications (2007, 2006, 2005, 2004, 2003, 2002, 2001)

2007

McMahon N., Crane M., Ruskin H.J. and Crane L. (2007), The Importance of Boundary Conditions in the Simulation of Dissolution in the USP Apparatus., Simulation Modelling Practice and Theory, 15(3):247-255, March 2007.

2006

Callaghan A. (2006). Emergent Properties of the Human Immune Response to HIV Infection: Results from Multi-Agent Computer Simulations, ERCIM News No. 64, January 2006.

Hecquet D., Ruskin H.J. and Crane, M. (2006). Optimisation and parallelisation strategies for Monte-Carlo simulation of HIV Infection, to appear in Computers in Biology and Medicine.

O'Leary C., Humphrys M. and Walshe R. (2006). Collaborative Online Development of Modular Intelligent Agents, ERCIM News No. 64, January 2006.

Perrin D. (2006). Agent-Based Modelling of Viral Infection, ERCIM News No. 64, January 2006.

Perrin D., Ruskin H.J., Burns J. and Crane M. (2006). An agent-based approach to immune modelling, 2006 International Conference on Computational Science and its Applications (ICCSA 2006), M. Gavrilova et al. (Eds.): ICCSA 2006, LNCS 3980, pp. 612-621, 2006.

Ruskin H. and Burns J. (2006). Network Emergence in Immune System Shape, ERCIM News No. 64, January 2006.

Ruskin H. and Burns, J. (2006). Weighted networks in immune system shape space, Physica A, The Journal of Statistical Mechanics and its Applications, 365(2):549-555, 2006.

Ruskin H. and Walshe R. (2006). Introduction to the Special Theme, ERCIM News No. 64, January 2006.

Walshe R. (2006). Modelling Bacterial Growth Patterns in the presence of Antibiotic, In Proceedings of 11th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS 2006), IEEE Computer Society, pp 177-186.

2005

Callaghan A. (2005). Agent-Based Modelling applied to HIV/AIDS, ERCIM News No. 60, January 2005.

Kerr G. (2005). BAIT: Bacteria - Antibiotic Interaction Tool, ERCIM News No. 60, January 2005.

Ruskin, H., Burns, J., Weighted networks in immune system shape space To appear in: Physica A, The Journal of Statistical Mechanics and Its Applications.

Ruskin, H., Burns, J., 2005. Network Emergence in Immune System Shape Space, Gervasi O., et al. (eds.): Lecture Notes in Computer Science, Vol. 3481. Springer-Verlag, Berlin Heidelberg New York (2005) 1254-1263.

2004

Burns, J. and Ruskin, H. (2004) Network Topology in Immune System Shape Space, In: Bubak, M.; Albada, G.D.v.; Sloot, P.M.A.; Dongarra, J. (Eds.): Lecture Notes in Computer Science, Vol. 3038. Springer-Verlag Pg. 1094-1101

Burns, J. and Ruskin, H. (2004) Diversity Emergence and Dynamics During Primary Immune Response: A Shape Space, Physical Space Model. Theory in Biosciences, Vol 123/2 Pg 183-194, Elsevier

Burns, J., Ruskin, H., (2004), A Stochastic Model of the Effector T Cell Lifecycle, In: Sloot P.M.A., Chopard, B. and Hoekstra A.G., (eds.): Cellular Automata, Lecture Notes in Computer Science, Vol. 3305. Springer-Verlag, Berlin Heidelberg (2004) 454-463

Crane, M., Crane, L., Healy, A.M., Corrigan, O.I., Gallagher, K.M. and McCarthy, L.G., (2004) A Pohlhausen Solution for the Mass Flux From a Multi-layered Compact in the USP Drug Dissolution Apparatus, Simulation Modelling Practice and Theory (SIMP&T), Vol. 12/6 Pg 397-411, Elsevier, 2004

Crane M., Hurley N., Crane L., Healy A.M., Corrigan, O.I., Gallagher, K.M. and McCarthy, L.G. (2004) Simulation of the USP drug delivery problem using CFD: experimental, numerical and mathematical aspects. to appear in Simulation Modelling Practice and Theory (SIMP&T), Vol. 12/2 Pg 147-158, Elsevier

Feng Y., Ruskin H.J. and Liu Y., (2004) Multiple Parameterisation of Human Immune Response in HIV: Many-Cell Models., Proceedings of the International Conference on Computational Science and Its Applications - ICCSA 2004, Laganà, A.; Gavrilova, M.L.; Kumar, V.; Mun, Y.; Tan, C.J.K.; Gervasi, O. (Eds.), Lecture Notes in Computer Science, Springer, May 2004, Vol. 3045, Pg 498-507, ISBN: 3-540-22057-7

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

2003

Burns J., Ruskin H.J. (2003) A Model of Immune Suppression and Repertoire Evolution. Proceedings of the International Conference on Computational Science 2003, (ICCS03), St. Petersburg, Russia, June 1-4.

Burns J., Ruskin H.J. (2003) Viral Strain Diversity and Immune Response - a Computational Model. Proceedings of the IASTED International Conference on Biomedical Engineering, Salzburg, Austria, June 25-27, 2003

McMahon N., Crane M., Ruskin H.J. and Crane L. (2003) The Mechanics of Drug-Dissolution. Proceedings in Applied mathematics and Mechanics (PAMM), Vol. 3, Issue 1, December 2003, p. 392-393.

2002

Liu Y. and Ruskin H. J. (2002) A Mesoscopic Approach to Modelling Immunological Memory. International Conference on Computational Science ICCS 2002, (Ed. Sloot P.M. A. et al.) pub. in Lecture Notes in Computer Science, LNCS (2002) 2329, 127. Springer-Verlag ISBN 3-540-43592, ISSN 0302-9743

Mannion R., Ruskin H.J. and Pandey R.B. (2002) Effects of Viral Mutation on Cellular Dynamics in a Monte Carlo Simulation of HIV Immune Response Model in Three Dimensions, Theory in Biosciences 121, 237, Elsevier

Ruskin H.J. , Pandey R.B. and Liu Y. (2002) Viral load and stochastic mutation in a Monte Carlo simulation of HIV. Physica A 311, 213, Elsevier

2001

Hurley, N., Crane, L., Crane, M., Healy, A.M., Corrigan, O.I., Gallagher, K.M. and McCarthy, L.G., Modelling drug delivery systems using finite element analysis, in Proceedings of the 4th International Eurosim 2001 Congress, Delft, June 2001 (ISBN: 90-806441-1-0).

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

Presentations (2007, 2006, 2005, 2004, 2003, 2002)

2007

Perrin D., Duhamel C., Ruskin H.J. and Crane M., Microarray biclustering: mathematical model and metaheuristic alternatives, accepted for the International Conference on Computational Methods (ICCM2007), Hiroshima, Japan, April 4-6 2007.

2006

Perrin D., Ruskin H.J., Burns J. and Crane M., An agent-based approach to immune modelling, 2006 International Conference on Computational Science and its Applications (ICCSA 2006), Glasgow, UK, May 8-11 2006.

Perrin D. and Ruskin H.J., Agent-Based Modelling of Viral Infection: An Introduction, poster presented at the BioNet 2006 conference, Tallaght, Ireland, January 18-19 2006.

Perrin D., Ruskin H.J. and Crane M. (2006). HIV Modelling - Parallel Implementation Strategies, accepted for presentation at the 3rd International Conference on Cluster and Grid Computing Systems (CGCS'06).

Perrin D., Ruskin H.J. and Crane M., 2006. An agent-based approach to immune modelling, Priming individual response, accepted for presentation at the 3rd International Conference on Modeling and Simulation (ICMS'06).

Ruskin, H.J., The Work of the Biocomputation Research Lab., at Waterford Inst. Technology, Ireland, January 25th.

Ruskin, H.J., Biocomputation: Cell to System, at National University of Ireland Maynooth, Feb. 24th.

2005

Barat, A., Ruskin, H.J, Crane, M., Modelling the in vitro Dissolution of Soluble Binary Drug Delivery Systems using Direct Monte Carlo techniques, accepted for presentation at First Open International Conference on Modelling and Simulation, Clermont-Ferrand, France, June 2005

McMahon, N., Crane, M., Ruskin, H.J, Crane, L., Particle Tracking: from Raindrops in 1940 to Drug Dissolution in 2005 accepted for presentation at Third MIT Conference on Computational Fluid and Solid Mechanics, Cambridge, Mass., June 2005

Ruskin, H.J., February 16th 2005. "BioComputation: Imitation and Inspiration", Speaker at Bioinformatics Inform 2005, DCU.

Ruskin, H.J., February 17th 2005. Speaker at Virtual Inst. Bioinformatics_Eire Bi-Annual Meeting, Biocomputation Group, DCU.

Ruskin, H.J., June 7th 2005. "Chip, Bytes and Bio: Computational and Mathematical Modelling of Complex Biosystems", Weill Medical College, Cornell University, NY, USA

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

2004

December 2004, Kerr, G., (w. R. Walshe, M. Duggan, C. Pender, R. Winters), at Annual BioNet Conference, Institute of Technology Carlow, The BAIT Simulation: Bacteria Antibiotic Interaction Tool

November 2004, Barat, A., (w. M. Crane, & H.J. Ruskin), at Irish Association for High Performance Computing Symposium, Monte Carlo and Cellular Automata Techniques in Simulating Drug Dissolution

October 2004, J. Burns, (w. H. Ruskin) at Sixth International conference on Cellular Automata for Research and Industry (ACRI 04), Amsterdam, The Netherlands, "A Stochastic Model of the Effector T Cell Lifecycle".

July 2004, A. Barat (w. M. Crane, H.J. Ruskin & A.-M. Healy) at EXYSTENCE Thematic Institute: From Many-Particle Physics to Multi-Agent Systems, Max Planck Institute for the Physics of Complex Systems (MPIPKS), Dresden, Germany, "Monte-Carlo models of dissolution of multi-component tablets in the USP paddle apparatus"

May 2004, Y. Feng, (w. H.J. Ruskin, Y. Liu) at International Conference on Computational Science & Applications (ICCSA04), Assisi, Italy, "Multiple Parameterisation of Human Immune Response in HIV: Many-Cell Models."

2003

June 2003 - J. Burns (w. H. Ruskin) at IASTED International Conference on Biomedical Engineering, Saltzburg, Austria. "Viral Strain Diversity and Immune Response - a Computational Model"

June 2003 - J. Burns (w. H. Ruskin) at International Conference on Computational Science, St. Petersburg, Russia. "A Model of Immune Suppression and Repertoire Evolution"

March 2003 - N. McMahon (w. H. Ruskin, M. Crane, L. Crane.) at GAMM, Padua, Italy - "Drug Dissolution Models"

2002

Sep 2002 - J. Burns (w. Heather Ruskin) at the 7th Granada Seminar on Complex Systems, Spain - "MC model of Immune Suppression and T-cell receptor cross-reactivity during primary response"

May/June 2002 - H. Ruskin (translation Y. Feng) at Dalian University of Technology, Dept. of Computer Science. 3 invited lectures on "Modelling & Scientific Computing in CA" and related topics

April 2002 - Y. Liu (w. H. Ruskin) at the International Conference on Computational Science, Amsterdam, The Netherlands - "A Mesoscopic Approach to modelling Immunological Memory"

Submissions Currently Under Review

Benoist, M., Murphy, J., Ruskin. H.J. and Crane, M., 2004. The management of Microarray data: The MIAME model, submitted to Information and Software Technology

Murphy J.T. and Walshe R., 2006. Micro-Gen: An Agent-Based Model of Bacteria-Antibiotic Interactions in Batch Culture, submitted to European Simulation and Modelling Conference, Toulouse, France.