Concepts -- Systems Biology Approaches: Solving New Puzzles in a Symphonic Manner -- Current Progress in Static and Dynamic Modeling of Biological Networks -- Getting Started in Biological Pathway Construction -- From Microarray to Biology -- Modeling and Reconstruction -- Computational Procedures for Model Identification -- Assembly of Logic-Based Diagrams of Biological Pathways -- Automating Mathematical Modeling of Biochemical Reaction Networks -- Strategies to Investigate Signal Transduction Pathways with Mathematical Modelling -- Inferring Transcriptional Regulatory Network -- Finding Functional Modules -- Modeling the Dynamics of Biological Networks from Time Course Data -- Decision Making in Cells -- Robustness of Neural Network Models -- Functional Modules in Protein-Protein Interaction Networks -- Mixture Model on Graphs: A Probabilistic Model for Network-Based Analysis of Proteomic Data -- Integration of Network Information for Protein Function Prediction -- Applications for Signaling Networks -- Cellular-Level Gene Regulatory Networks: Their Derivation and Properties -- Tyrosine-Phosphoproteome Dynamics -- Systems Biology of the MAPK1,2 Network -- Pathway Crosstalk Network -- Crosstalk Between Mitogen-Activated Protein Kinase and Phosphoinositide-3 Kinase Signaling Pathways in Development and Disease -- Systems-Level Analyses of the Mammalian Innate Immune Response -- Molecular Basis of Protective Anti-Inflammatory Signalling by Cyclic AMP in the Vascular Endothelium -- Construction of Cancer-Perturbed Protein-Protein Interaction Network of Apoptosis for Drug Target Discovery -- Transcriptional Changes in Alzheimer's Disease -- Pathogenesis of Obesity-Related Chronic Liver Diseases as the Study Case for the Systems Biology -- The Evolving Transcriptome of Head and Neck Squamous Cell Carcinoma -- Peptide Microarrays for a Network Analysis of Changes in Molecular Interactions in Cellular Signalling -- Tools for Systems Biology -- A Primer on Modular Mass-Action Modelling with CellML -- FERN - Stochastic Simulation and Evaluation of Reaction Networks -- Programming Biology in BlenX -- Discrete Modelling: Petri Net and Logical Approaches -- ProteoLens: A Database-Driven Visual Data Mining Tool for Network Biology -- MADNet: A Web Server for Contextual Analysis and Visualization of High-Throughput Experiments -- Erratum to: Functional Modules in Protein-Protein Interaction Networks.