Systems Biology

The rapidly developing methods of systems biology can help investigators in various areas of modern biomedical research to make inference and predictions from their data that intuition alone would not discern. Many of these methods, however, are commonly perceived as esoteric and inaccessible to biomedical researchers: Even evaluating their applicability to the problem at hand seems to require from the biologist a broad kno- edge of mathematics or engineering. This book is written by scientists who do possess such knowledge, who have successfully applied it to biological problems in various c- texts, and who found that their experience can be crystallized in a form very similar to a typical biological laboratory protocol. Learning a new laboratory procedure may at first appear formidable, and the int- ested researchers may be unsure whether their problem falls within the area of applicability of the new technique. The researchers will rely on the experience of others who have condensed it into a methods paper, with the theory behind the method, its step-by-step implementation, and the pitfalls explained thoroughly and from the practical angle. It is the intention of the authors of this book to make the methods of systems biology widely understood by biomedical researchers by explaining them in the same proven format of a protocol article.

This book presents numerous methods on how to effectively apply quantitative systems methodology to biological research. Each chapter contains the theory behind a method, step-by-step implementation, and a discussion of possible pitfalls to avoid.

Written by leading scientists who apply quantitative systems methodology in their biological research

Introduction: A Practical Guide to the Systems Approach in Biology.- Methods for Analyzing Biomolecular Systems.- Computational Modeling of Biochemical Networks Using COPASI.- Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks.- Modeling Molecular Regulatory Networks with JigCell and PET.- Rule-Based Modeling of Biochemical Systems with BioNetGen.- Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks.- Spatial Analysis and Control of Cellular Processes.- Microfluidics Technology for Systems Biology Research.- Systems Approach to Therapeutics Design.- Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models.- A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics.- Location Proteomics: Systematic Determination of Protein Subcellular Location.- Methods for Larger-Scale Systems Analysis.- Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit.- Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment.- BioLogic: A Mathematical Modeling Framework for Immunologists.- Dynamic Knowledge Representation Using Agent-Based Modeling: Ontology Instantiation and Verification of Conceptual Models.- Systems Biology of Microbial Communities.