Note: Intro -- Combining a High-Throughput Bioinformatics Grid andBioinformatics Web Services -- Introduction -- Materials and Methods -- Architecture -- Data Flow Implementation -- Results and Discussion -- Conclusion -- References -- Using Public Resource Computing and SystematicPre-calculation for Large Scale Sequence Analysis -- Introduction -- Public Resource Computing -- Systematic Pre-calculation of Sequence Analyses -- Systems and Methods -- Implementation -- BOINC Server -- BOINC Applications -- Results -- Performance of BOINC-Applications -- The BOINCSIMAP Project -- Conclusion -- Availability -- References -- Accelerated microRNA-Precursor DetectionUsing the Smith-Waterman Algorithm onFPGAs -- Introduction -- Previous Work -- FPGA in Bioinformatics -- Detecting microRNA Precursor Sequences with Smith-Waterman -- Scanning a Single Genomic Sequence -- Comparative Application -- Results -- Biological Relevance -- Interfacing of the Smith-Waterman Accelerator to LiSA -- Computational Performance -- Summary and Conclusion -- Implementation of a Distributed Architecture forManaging Collection and Dissemination of Data for FetalAlcohol Spectrum Disorders Research -- Introduction -- Distributed Nature of CIFASD -- Commitment to Data Integration -- Clinical Needs vs. Computer Science Research -- System Design -- Data Dictionaries -- Data Entry -- Central Repository and Data Flow -- Assuring Data Quality -- Reliable Infrastructure -- Results and Conclusions -- References -- Grid-Enabled High Throughput Virtual Screening -- Introduction -- Large Scale in Silico Docking Against Malaria -- Introduction -- Objectives -- In Silico Docking Against Avian Influenza -- Introduction -- Objectives -- The Grid Tools -- The Grid Infrastructures -- The WISDOM Production Environment -- The DIANE Framework -- Results -- WISDOM Results -- Perspectives. , Perspective on the Grid Side: WISDOM-II -- From Virtual Docking to Virtual Screening -- Conclusion -- References -- Grid Computing for the Estimation of Toxicity:Acute Toxicity onFathead Minnow (Pimephales promelas) -- Introduction -- Predictive Models for the Toxicity Prediction -- Grid Computing for Prediction Models -- Estimation of Acute Toxicity on Fathead Minnow -- Experimental Data -- Molecular Structures -- Molecular Descriptors -- Forward Selection of Descriptors to Multi-linear Regression -- Heuristic Back-Propagation Neural Networks for QSAR -- Results and Discussion -- Model Based on Multi-linear Regression -- Model Based on Artificial Neural Networks -- Comparison with Previously Published Models -- Conclusions -- Peer-to-Peer Experimentation in ProteinStructure Prediction: An Architecture,Experiment and Initial Results -- Introduction: Peer-to-Peer Experimentation -- Scientists as Peers in a Web Community -- Scientific Coordination as Peer-to-Peer Communication -- Experiment Implementation -- The MagentA Architecture -- Example Experiment: Consistency-Checking in Protein Structure Prediction -- 3-D Structural Models for Yeast Proteins -- Data Sources -- Processing/Pre-filtering of Data Sets -- Consistency-Checking -- Results and Discussion -- Conclusions and Future Work -- Gene Prediction in Metagenomic Libraries Usingthe Self Organising Map and High PerformanceComputing Techniques -- Introduction -- Rationale for the SOM -- The SOM -- Descriptor -- Analysis -- Parallel Approach -- MPI Implementation -- Annotation -- Results -- Conclusions -- A Distributed System for Genetic Linkage Analysis -- Introduction -- The Grid Execution Hierarchy Scheduling Algorithm -- Grid Execution Hierarchy -- Scheduling Tasks in Grid Hierarchy -- Handling Multiple Grids at the Same Level of the Execution Hierarchy. , Parallel Algorithm for the Computation of LOD Score -- Serial Algorithm -- Parallel Algorithm -- Implementation of the Parallel Algorithm for Execution in Grid Hierarchy -- Deployment of SUPERLINK-ONLINE -- Results -- Parallel Algorithm Performance -- Performance of the Grid Execution Hierarchy Scheduling Algorithm -- Related Work and Conclusions -- References -- Enabling Data Sharing and Collaboration inComplex Systems Applications -- Introduction -- Data Sharing Methods -- Objective -- An Example -- Characteristics of Our Network -- Resource Management and Grouping -- Security -- Scalability -- Performance -- Fairness -- Design Issues -- Content Storage and Management -- Network Structure -- Access Controls and Secure Storage -- Content Replication and Accountability -- Architecture and Implementation -- The Data -- The Database -- Database Interface -- User Interface Layer -- Practical Details -- Database Creation and Roles -- Security -- Installing and Connecting -- Performance -- Other Configuration Issues -- Conclusions -- Accessing Bio-databases with OGSA-DAI -A Performance Analysis -- Introduction -- OGSA-DAI -- Methods -- Results -- Hardware and Software Configuration -- Loading Data -- Retrieving Data -- Conclusion -- Systems Support for Remote Visualization of GenomicsApplications over Wide Area Networks -- Introduction -- System Overview -- Compressing 2-D Pixel Segments -- Basic Compression Algorithm -- Content-Based Anchoring of 2-D Pixel Segments -- An Optimization with Two-Level Fingerprinting -- Implementation -- Evaluation -- Experimental Testbed -- Network Communication Requirements -- Compression Results -- Related Work -- Conclusion -- References -- HVEM DataGrid: Implementation of a BiologicData Management System for Experiments withHigh Voltage Electron Microscope -- Introduction -- Related Works -- Background. , HVEM DataGrid System -- System Architecture and Design -- Schema of HVEM DataGrid -- Data Workflow -- Data Management and Access -- Data Search -- System Implementation -- Environmental Setup -- DataGrid Test -- Conclusion and Future Work.