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 Drug-Dissolution

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. Up-sizing 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.