This book constitutes the refereed proceedings of the Second International Symposium on Computational Life Sciences, CompLife 2006, held in Cambridge, UK, in September 2006. The 25 revised full papers presented were carefully reviewed and selected from 56 initial submissions. The papers are organized in topical sections on genomics, data mining, molecular simulation, molecular informatics, systems biology, biological networks/metabolism, and computational neuroscience. This book constitutes the refereed proceedings of the Second International Symposium on Computational Life Sciences, CompLife 2006. The 25 revised full papers presented were carefully reviewed and selected from 56 initial submissions. The papers are organized in topical sections on genomics, data mining, molecular simulation, molecular informatics, systems biology, biological networks/metabolism, and computational neuroscience. Genomics Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering 1 Michael Hirsch, Allan Tucker, Stephen Swift, Nigel Martin, Christine Orengo, Paul Kellam, Xiaohui Liu A Hybrid Grid and Its Application to Orthologous Groups Clustering 11 Tae-Kyung Kim, Kyung-Ran Kim, Sang-Keun Oh, Jong-Hak Lee, Wan-Sup Cho Promoter Prediction Using Physico-Chemical Properties of DNA 21 Philip Uren, R. Michael Cameron-Jones, Arthur Sale Parametric Spectral Analysis of Malaria Gene Expression Time Series Data 32 Liping Du, Shuanhu Wu, Alan Wee-Chung Liew, David Keith Smith, Hong Yan An Efficient Algorithm for Finding Long Conserved Regions Between Genes 42 Tak-Man Ma, Yuh-Dauh Lyuu, Yen- Wu Ti The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders 52 Matthias Bernt, Daniel Merkle, Martin Middendorf Data Mining Building Structure-Property Predictive Models Using Data Assimilation 64 Hamse Y. Mussa, David J. Lary, Robert C. Glen Set-Oriented Dimension Reduction: Localizing Principal Component Analysis Via Hidden Markov Models 74 Illia Horenko, Johannes Schmidt-Ehrenberg, Christof Sch tte Relational Subgroup Discovery for Descriptive Analysis of Microarray Data 86 Igor Trajkovski, Filip elezn , Jakub Tolar, Nada Lavrac Applicability of Loop Recombination in Ciliates Using the Breakpoint Graph 97 Robert Brijder, Hendrik Jan Hoogeboom, Michael Muskulus High-Throughput Identification of Chemistry in Life Science Texts 107 Peter Corbett, Peter Murray-Rust Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level 119 Tim O.F. Conrad, Alexander Leichtle, Andre Hageh lsmann, Elmar Diederichs, Sven Baumann, Joachim Thiery, Christof Sch tte Molecular Simulation Dynamic Complexity of Chaotic Transitions in High-Dimensional Classical Dynamics: Leu-Enkephalin Folding 129 Dmitry Nerukh, George Karvounis, Robert C. Glen Solvent Effects and Conformational Stability of a Tripeptide 141 Maxim V. Fedorov, Stephan Schumm, Jonathan M. Goodman Grid Assisted Ensemble Molecular Dynamics Simulations of HIV-1 Proteases Reveal Novel Conformations of the Inhibitor Saquinavir 150 S. Kashif Sadiq, Stefan J. Zasada, Peter V. Coveney Molecular Informatics A Structure-Based Analysis of Single Molecule Force Spectroscopy (MFS) Data for Bacteriorhodopsin and Four Mutants 162 Annalisa Marsico, K. Tanuj Sapra, Daniel J. Muller, Michael Schroeder, Dirk Labudde Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint 173 Edward O. Cannon, John B.O. Mitchell A Point-Matching Based Algorithm for 3D Surface Alignment of Drug-Sized Molecules 183 Daniel Baum, Hans-Christian Hege Systems Biology Adaptive Approach for Modelling Variability in Pharmacokinetics 194 Andrea Y. Wei , Illia Horenko, Wilhelm Huisinga A New Approach to Flux Coupling Analysis of Metabolic Networks 205 Abdelhalim Larhlimi, Alexander Bockmayr Biological Networks/Metabolism Software Supported Modelling in Pharmacokinetics 216 Regina Telgmann, Max von Kleist, Wilhelm Huisinga On the Interpretation of High Throughput MS Based Metabolomics Fingerprints with Random Forest 226 David P. Enot, Manfred Beckmann, John Draper Construction of Correlation Networks with Explicit Time-Slices Using Time-Lagged, Variable Interval Standard and Partial Correlation Coefficients 236 Wouter Meuleman, Monique C.M. Welten, Fons J. Verbeek Computational Neuroscience The Language of Cortical Dynamics 247 Peter Andras A Simple Method to Simultaneously Track the Numbers of Expressed Channel Proteins in a Neuron 257 A. Aldo Faisal, Jeremy E. Niven Author Index 269