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. Systems biology is a new and exciting field that is an extension of many others including: Molecular Biology, Immunology, Genetics, Computational Biology, and Mathematical Biology. The goal is to understand the relationships from genes to organisms through networks in biological systems. The series Systems Biology examines an array of topics, in systems biology studies, ranging from molecular parts of cells to network modeling. The first volume in this series, Systems Biology of Signaling Networks, contains a collection of work in regulatory signaling networks and the use of large-scale omics data.