BIOCOMPUTATION PROJECTS

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BIOCOMPUTATION PROJECTS

• Modelling and Scientific Computing Research
  Group,
• School of Computing, DCU

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CURRENT

• Drug-Dissolution- Analytical
• - MC
• Immune Response Modelling
• - MC/CA
• - Graphical/Nets
• Microarray - SVD
• - GA/EC

Parallel/ Distributed underpinning
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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)

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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

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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

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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.