Dublin City University, Ireland

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The Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM) is a multi-disciplinary research institute based at Dublin City University. Founded in 2007, SCI-SYM has applied a variety of modelling techniques (probabilistic, mathematical and semi-analytical) aided by state-of-the-art HPC Systems to a number of research areas including Bioinformatics, Biomedical Systems, Astrophysics and Social/Environmental Modelling. Researchers at SCI-SYM have worked closely with industrial partners such as IBM, Cray Inc., Airtricity, Icon Plc, Quintiles, Elan Corporation, and Research Institutions such as National Institutes for Health, the German Cancer Research Center (DKFZ) and Hospital for Special Surgery, NY.


Profile of staff members and previous experience

Dr. Martin Crane is a Senior Lecturer in the School of Computing, Dublin City University with considerable experience in the simulation and modelling of bio-related problems such as drug dissolution (in vitro and in vivo), microarray data analysis and the application of time series analysis to EEG data for epilepsy. Previous funded drug dissolution research has involved EU-funded research on use of HPC in the design of Novel Drug Delivery Systems with Elan Corporation, HEA PRTLI funded work on dissolution in different environments, Design and Optimization of Biomedical Implants and Design of proprietary drug delivery mechanisms for IBS/Crohns disease, in collaboration with Sigmoid Pharma using HPC.


Heather J. Ruskin B.Sc., M.Sc., Ph. D. (1993), CStat. (FRSS), CPhys. FInstP. is a Professor in the School of Computing, DCU. Her principal areas of research are in Modelling and Scientific Computing, i.e.; computational models, including stochastic cellular automata, Monte Carlo and variants, of spatiotemporal processes in physical, biological and related systems; statistical modelling applications in the natural and medical sciences. She is a Chartered Statistician, (formerly designated Fellow of the Royal Statistical Society), a Chartered Physicist and member of the Institute of Physics and European Phys. Soc., the International Biometrics Society and Association of Researchers in Medicine and Science. She has published over 100 papers in refereed journals, 20 refereed abstracts /conference presentations/chapters in international conference proceedings, as well as a number of limited circulation reports for e.g. state funded institutions etc.


Ray Walshe is Research Technical Lead for The Irish Cloud Technology Centre( IC4). He has been a lecturer in the School of Computing in Dublin City University for 17 years and his research interests are High Performance Computing, GRID Computing, Exascale, Cloud and Big Data Computing with specific interest in Agent-based Models, Scientific Computing, Systems Modelling, Artificial Intelligence and Systems Biology. Ray is Director of CloudCORE Research Centre at DCU and Deputy Director SCI-SYM Research Centre at Dublin City University. He specialises in industry engagement and has a number of active industry and research funded projects in Cloud Exascale Data and Mobile Cloud Networks.


Dr Mary J. O'Connell BSc (Hons) PhD (2005), is a lecturer in the School of Biotechnology, Dublin City University. Her area of research is evolutionary medicine and the molecular evolution of vertebrates. Her research spans both data analysis and theory development. Her expertise is in the analysis of complete vertebrate genomes; the emergence of novel species-specific regulatory elements; phylogenomics; and, protein functional shift. These feed into her focus of evolutionary medicine - predicting the suitability of certain model organisms to human disease using evolutionary modeling. Her research is currently funded by Science foundation Ireland, HEA PRTLI, IRCSET, the Walsh fellowship, and Pierse Trust and O'Hare scholarships. She is a Genome 10K affiliate and has worked closely with international consortia on novel genome assembly and analysis. Her publications in international peer reviewed journals are available to view through her lab website: http://bioinf.dcu.ie.


Dr Turlough Downes is Director of the Computational Science and Complex Modelling Centre (SCI-SYM) in Dublin City University and is Chair of the Programme Committee of the PRACE User Forum. He is a Senior Lecturer in the School of Mathematical Sciences, Dublin City University and has a joint affiliation with the Dublin Institute for Advanced Studies. His main area of expertise is computational astrophysics, with a particular emphasis on turbulence in star forming regions and on non-thermal particle acceleration around supernova blastwaves. He is an expert on coding for massively parallel systems: his research group, funded by national, European and international agencies, designed and developed the HYDRA multifluid MHD code which displays excellent strong scaling properties up to petascale systems.



Bioinformatics and Molecular Evolution Group at Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM)



Five recent publications relevant to the project

1) Downes, T.P., O'Sullivan, S., 2011, Multifluid magnetohydrodynamic turbulent decay, The Astrophysical Journal, 730, 12-23.730, 12-23.


2) Loughran NB, McCormick-Hill S, Hinde S, Leidal KG, Bloomberg S, Loughran ST, O¹Connor B, Ó Fágáin C, Nauseef WM*, and O¹Connell MJ*. ³Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase². Molecular Biology and Evolution (Impact Factor 8.9)


3) Perrin D., Ruskin H.J., Crane M., 2010, Model refinement through high-performance computing: an agent-based HIV example. Immunome Research 2010, 6(Suppl 1):S3, (Impact Factor 5.33)


4) Walshe, R.J., Ruskin, and Callaghan, A., 2008, Multi-agent simulations of the immune response to HIV during the acute stage of infection. International Journal Of Modern Physics C:Physics And Computers, 19, l,pp!5-32.


5) Barat, A., Crane, M., Ruskin, H.J., 2009, Quantitative multi-agent models for simulating protein release from PLGA bioerodible nano-and microspheres, Journal of pharmaceutical and biomedical analysis 48 (2), 361-368.