Download biocomputation projects

BIOCOMPUTATION
PROJECTS
Modelling and Scientific Computing
Research Group,
School of Computing, DCU
CURRENT
• Drug-Dissolution- Analytical
- MC
• Immune Response Modelling
- MC/CA
- Graphical/Nets
• Microarray
- SVD
- GA/EC
Parallel/
Distributed
underpinning
CURRENT STRENGTHS
• New Lamps for Old http://www.computing.dcu.ie/~msc/cluster/ .
New PC cluster 2004. For Monte-Carlo, Drug-dissolution,
Microarrays and Bioinformatics work. Taught Masters programme.
• Funding - DCU, Enterprise Ireland, HEA PRTLI - National
Institute for Cellular Biotechnology, EU COST.
• Researchers - main group strength - approx. 20 academics, PG.
Biocomputation core - in collaboration with Biotech., Chemistry
colleagues, (DCU), through National Institute Cellular Biotechnology,
Dr. A-M. Healy, (TCD), Prof. R. Pandey (USM/Stennis)
PEOPLE
PROFILES in BRIEF
• Heather J. Ruskin Statistical and Computational Modelling for
Complex Systems. (MC in Bio, Physics and Finance, Socio-economic)
• Martin Crane Biocomputation (Drug-Dissolution Models,
Pharmacology, Microarray, Financial Models.
• Yu Feng Froth Dynamics,Computer Simulation Methods
• John Burns Computational Methods in I.R. Models /Monte Carlo
• Niall McMahon Drug-Dissolution Models
• Karl Podesta Parallel Solutions/Distributed systems in Bioinformatics
• Ana Barat Drug-Dissolution and Monte Carlo, Microarray
• C. Ooi Microarray, GA and Evolutionary Computation
Agent-based models for Artificial Life
Further background details : provided
RECENT PUBLICATIONS
• Drug-Dissolution Crane M., Crane L., Healy A.-M., Corrigan O.J.,
Gallagher K.M., McCarthy L.G. (2003). "A Pohlhausen Solution for
the Mass Flux from a Multi-Layered Compact in the USP DrugDissolution Apparatus."
McMahon N.,M., Crane M., Ruskin H.J. , Crane L. to appear PAMM
(2003) "The Mechanics of Drug Dissolution" Wiley Interscience
• Immune Response Mannion R., Ruskin H.J. and Pandey R.B. (2002)
Theor. Biosc. 121, 237. "Effects of Viral Mutation on Cellular
Dynamics in a Monte Carlo Simulation of HIV Immune Response
Model in Three Dimensions."
Burns, J., Ruskin, H. J.(2003) "A Model of Immune Suppression and
Repertoire Evolution." (ICCS03), St. Petersburg, Russia, June 2003
Springer Lecture Notes in Computer Science (in Press).
• Others : Sample papers provided
PROJECTED WORK PLAN
2004-2006
• Drug-Dissolution: Analytical and Monte Carlo on tablet
drug/excipient layers, drug/excipient matrix. Video experiments of
fragmentation size informing distributional choice for MC/Bayesian
• Immune Response: Diversity emergence and dynamics during
primary response. Hybrid physical/shape-space validation. Persistence
into secondary and critical endpoints. Progression blueprinted. Upsizing and scalability - parallel options. Network topology and a vision
of shape-space mechanics.
• Parallel - implementations of common sequence analysis tools EMBOSS and others. Cluster-computing and bio-system modelling.
• Microarray network inference in time series mA data, (evolutionary
algorithms). Co-regulation of genes borrowed from co-movement of
financial stoocks. The case for co-operation and inter-connectivity.