Systems biology / edited by Ivan V. Maly. — New York, NY : Humana Press, c2009. – (58.17/M592/v.500) |
Contents
Contents
Preface
Contributors
PART I: INTRODUCTION
1 Introduction: A Practical Guide to the Systems Approach in Biology
PART II: METHODS FOR ANALYZING BIOMOLECULAR SYSTEMS
2 Computational Modeling of Biochemical Networks Using COPASI
3 Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks
4 Modeling Molecular Regulatory Networks with JigCell and PET
5 Rule-Based Modeling of Biochemical Systems with BioNetGen
6 Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks
PART III: SPATIAL ANALYSIS AND CONTROL OF CELLULAR PROCESSES
7 Microfluidics Technology for Systems Biology Research
8 Systems Approach to Therapeutics Design
9 Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models
10 A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics
11 Location Proteomics: Systematic Determination of Protein Subcellular Location
PART IV: METHODS FOR LARGER-SCALE SYSTEMS ANALYSIS
12. Model-Based Global Analysis of Heterogeneous Experimental Data Using grit
13. Multicell Simulations of Development Simulation Environment and Disease Using the CompuCell3D
14. BioLogic: A Mathematical Modeling Framework for Immunologists
15. Dynamic Knowledge Representation Using Agent-Based Modeling: Ontology Instantiation and Verification of Conceptual Models 445
Systems Biology of Microbial Communities