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Title Page 2 Copyright Page 3 Table of Contents 7 EDITORS 9 CONTRIBUTORS 9 PREFACE 11 PART 1 Basic Concepts 13 Chapter 1 Introduction to Whole Cell Modeling 14 Introduction 14 Modeling Fundamentals 14 1. The Phenomenon 14 1.1 Map 14 1.2 Metabolic Pathways 16 1.2.1 IUBMB-Nicholson Minimaps 16 1.2.2 Boehringer Mannheim Biochemical Pathways 17 1.2.3 Kyoto Encyclopedia of Genes and Genomes (KEGG) 17 1.2.4 What Is There (WIT) 17 1.2.5 Enzyme and Metabolic Pathway (EMP) 17 1.2.6 Biopathways Consortium 17 1.2.7 EcoCyc 17 1.2.8 PathDB 18 1.2.9 The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) 18 1.2.10 Metavista 18 1.2.11 Metabolic Pathways in Biochemistry 18 1.2.12 THCME Medical Biochemistry 18 1.3 Regulatory Pathways 18 1.3.1 KEGG Regulatory Pathways 18 1.3.2 BioCarta 18 1.3.3 Biomolecular Interaction Network Database (BIND) 18 1.3.4 Signal Pathway Database, SPAD 19 1.3.5 Cell Signaling Networks Database, CSNDB 19 1.3.6 Munich Information Centre for Protein Sequences, MIPS 19 1.3.7 Wnt Signaling Pathway 19 1.3.8 Transpath 19 1.4 Transcription Factors 19 1.4.1 TRANSFAC—Transcription Factor Database 19 1.4.2 RegulonDB 19 1.4.3 DBTBS 20 1.4.4 SCPD 20 1.5 Gene Exp

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