Computational Life Sciences II [electronic resource] : Second International Symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings / edited by Michael R. Berthold, Robert C. Glen, Ingrid Fischer.

By: R. Berthold, Michael [editor.]Contributor(s): Glen, Robert C [editor.] | Fischer, Ingrid [editor.] | SpringerLink (Online service)Material type: TextTextLanguage: English Series: Lecture Notes in Computer Science: 4216Publisher: Berlin, Heidelberg : Springer Berlin Heidelberg, 2006Description: XIII, 269 p. Also available online. online resourceContent type: text Media type: computer Carrier type: online resourceISBN: 9783540457688Subject(s): Computer science | Medical records -- Data processing | Database management | Information storage and retrieval systems | Information systems | Proteomics | Bioinformatics | Computer Science | Information Storage and Retrieval | Health Informatics | Database Management | Information Systems Applications (incl.Internet) | Bioinformatics | ProteomicsAdditional physical formats: Printed edition:: No titleDDC classification: 025.04 LOC classification: QA75.5-76.95Online resources: Click here to access online
Contents:
Genomics -- Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering -- A Hybrid Grid and Its Application to Orthologous Groups Clustering -- Promoter Prediction Using Physico-Chemical Properties of DNA -- Parametric Spectral Analysis of Malaria Gene Expression Time Series Data -- An Efficient Algorithm for Finding Long Conserved Regions Between Genes -- The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders -- Data Mining -- Building Structure-Property Predictive Models Using Data Assimilation -- Set-Oriented Dimension Reduction: Localizing Principal Component Analysis Via Hidden Markov Models -- Relational Subgroup Discovery for Descriptive Analysis of Microarray Data -- Applicability of Loop Recombination in Ciliates Using the Breakpoint Graph -- High-Throughput Identification of Chemistry in Life Science Texts -- Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level -- Molecular Simulation -- Dynamic Complexity of Chaotic Transitions in High-Dimensional Classical Dynamics: Leu-Enkephalin Folding -- Solvent Effects and Conformational Stability of a Tripeptide -- Grid Assisted Ensemble Molecular Dynamics Simulations of HIV-1 Proteases Reveal Novel Conformations of the Inhibitor Saquinavir -- Molecular Informatics -- A Structure-Based Analysis of Single Molecule Force Spectroscopy (SMFS) Data for Bacteriorhodopsin and Four Mutants -- Classifying the World Anti-Doping Agency’s 2005 Prohibited List Using the Chemistry Development Kit Fingerprint -- A Point-Matching Based Algorithm for 3D Surface Alignment of Drug-Sized Molecules -- Systems Biology -- Adaptive Approach for Modelling Variability in Pharmacokinetics -- A New Approach to Flux Coupling Analysis of Metabolic Networks -- Biological Networks / Metabolism -- Software Supported Modelling in Pharmacokinetics -- On the Interpretation of High Throughput MS Based Metabolomics Fingerprints with Random Forest -- Construction of Correlation Networks with Explicit Time-Slices Using Time-Lagged, Variable Interval Standard and Partial Correlation Coefficients -- Computational Neuroscience -- The Language of Cortical Dynamics -- A Simple Method to Simultaneously Track the Numbers of Expressed Channel Proteins in a Neuron.
In: Springer eBooksSummary: Since our ?rstCompLife symposiumlast year,wehaveseenthe predicted trends inthelifeandcomputerscienceareascontinuewithever-increasingproductionof high-quality data mated to novel analysis methods. The integration of the most advanced computationalmethods into experimentaldesign and in particularthe validation of these methods will remain a challenge.However,there is increasing appreciation between the di?erent scienti?c communities in computer science and biology that each has substantial goals in common and much to gain by collaboration on complex problems. Providing a forum for an open and lively exchangebetweencomputerscientists,biologists,andchemistsremainsourgoal. Toencouragepreciselythistypeofexchange,crossingthebordersofthesciences, we organized the First Symposium on Computational Life Science in Konstanz, Germany in September 2005 (the proceedings were published in this series as LNBI3695).Duetothesuccessofthesymposium,especiallyinbringingtogether scientists with diversebackgrounds,a secondsymposium was held in Cambridge (September 27-29, 2006). The conference program shows that the scienti?c mix worked out very well again. We received higher quality submissions (56 this time) and selected 23 for oral presentation. As a supplement to the normal conference program we arranged for a “Free Software Session,” where a dozen open source tools and toolkits were presented. Due to the nature of such software projects it seemed inappropriate to cover them in printed form but the conference Web site will continue to link to the respective pages (www.complife.org). Adding this session to the symposium also educated attendees on how to use some of the methods presented and shed some light on the wealth of free tools available already.
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Genomics -- Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering -- A Hybrid Grid and Its Application to Orthologous Groups Clustering -- Promoter Prediction Using Physico-Chemical Properties of DNA -- Parametric Spectral Analysis of Malaria Gene Expression Time Series Data -- An Efficient Algorithm for Finding Long Conserved Regions Between Genes -- The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders -- Data Mining -- Building Structure-Property Predictive Models Using Data Assimilation -- Set-Oriented Dimension Reduction: Localizing Principal Component Analysis Via Hidden Markov Models -- Relational Subgroup Discovery for Descriptive Analysis of Microarray Data -- Applicability of Loop Recombination in Ciliates Using the Breakpoint Graph -- High-Throughput Identification of Chemistry in Life Science Texts -- Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level -- Molecular Simulation -- Dynamic Complexity of Chaotic Transitions in High-Dimensional Classical Dynamics: Leu-Enkephalin Folding -- Solvent Effects and Conformational Stability of a Tripeptide -- Grid Assisted Ensemble Molecular Dynamics Simulations of HIV-1 Proteases Reveal Novel Conformations of the Inhibitor Saquinavir -- Molecular Informatics -- A Structure-Based Analysis of Single Molecule Force Spectroscopy (SMFS) Data for Bacteriorhodopsin and Four Mutants -- Classifying the World Anti-Doping Agency’s 2005 Prohibited List Using the Chemistry Development Kit Fingerprint -- A Point-Matching Based Algorithm for 3D Surface Alignment of Drug-Sized Molecules -- Systems Biology -- Adaptive Approach for Modelling Variability in Pharmacokinetics -- A New Approach to Flux Coupling Analysis of Metabolic Networks -- Biological Networks / Metabolism -- Software Supported Modelling in Pharmacokinetics -- On the Interpretation of High Throughput MS Based Metabolomics Fingerprints with Random Forest -- Construction of Correlation Networks with Explicit Time-Slices Using Time-Lagged, Variable Interval Standard and Partial Correlation Coefficients -- Computational Neuroscience -- The Language of Cortical Dynamics -- A Simple Method to Simultaneously Track the Numbers of Expressed Channel Proteins in a Neuron.

Since our ?rstCompLife symposiumlast year,wehaveseenthe predicted trends inthelifeandcomputerscienceareascontinuewithever-increasingproductionof high-quality data mated to novel analysis methods. The integration of the most advanced computationalmethods into experimentaldesign and in particularthe validation of these methods will remain a challenge.However,there is increasing appreciation between the di?erent scienti?c communities in computer science and biology that each has substantial goals in common and much to gain by collaboration on complex problems. Providing a forum for an open and lively exchangebetweencomputerscientists,biologists,andchemistsremainsourgoal. Toencouragepreciselythistypeofexchange,crossingthebordersofthesciences, we organized the First Symposium on Computational Life Science in Konstanz, Germany in September 2005 (the proceedings were published in this series as LNBI3695).Duetothesuccessofthesymposium,especiallyinbringingtogether scientists with diversebackgrounds,a secondsymposium was held in Cambridge (September 27-29, 2006). The conference program shows that the scienti?c mix worked out very well again. We received higher quality submissions (56 this time) and selected 23 for oral presentation. As a supplement to the normal conference program we arranged for a “Free Software Session,” where a dozen open source tools and toolkits were presented. Due to the nature of such software projects it seemed inappropriate to cover them in printed form but the conference Web site will continue to link to the respective pages (www.complife.org). Adding this session to the symposium also educated attendees on how to use some of the methods presented and shed some light on the wealth of free tools available already.

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