Systems Biology

1. Front Matter

   Pages i-xi

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2. Introduction

   1. Front Matter

      Pages 1-1

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   2. Introduction: A Practical Guide to the Systems Approach in Biology

      • Ivan V. Maly

      Pages 1-11

3. Methods for Analyzing Biomolecular Systems

   1. Front Matter

      Pages 1-1

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   2. Computational Modeling of Biochemical Networks Using COPASI

      • Pedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada, Ursula Kummer

      Pages 17-59

   3. Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks

      • Matthew A. Oberhardt, Arvind K. Chavali, Jason A. Papin

      Pages 61-80

   4. Modeling Molecular Regulatory Networks with JigCell and PET

      • Clifford A. Shaffer, Jason W. Zwolak, Ranjit Randhawa, John J. Tyson

      Pages 81-111

   5. Rule-Based Modeling of Biochemical Systems with BioNetGen

      • James R. Faeder, Michael L. Blinov, William S. Hlavacek

      Pages 113-167

   6. Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks

      • Kerry J. Kim

      Pages 169-200

4. Spatial Analysis and Control of Cellular Processes

   1. Front Matter

      Pages 1-1

      PDF

   2. Microfluidics Technology for Systems Biology Research

      • C. Joanne Wang, Andre Levchenko

      Pages 203-219

   3. Systems Approach to Therapeutics Design

      • Bert J. Lao, Daniel T. Kamei

      Pages 221-236

   4. Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models

      • Jacob Czech, Markus Dittrich, Joel R. Stiles

      Pages 237-287

   5. A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics

      • Július Parulek, Miloš Šrámek, Michal Červęanský, Marta Novotová, Ivan Zahradník*

      Pages 289-312

   6. Location Proteomics: Systematic Determination of Protein Subcellular Location

      • Justin Newberg, Juchang Hua, Robert F. Murphy

      Pages 313-332

5. Methods for Larger-Scale Systems Analysis

   1. Front Matter

      Pages 1-1

      PDF

   2. Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit

      • Mikhail K. Levin, Manju M. Hingorani, Raquell M. Holmes, Smita S. Patel, John H. Carson

      Pages 335-359

   3. Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment

      • Maciej H. Swat, Susan D. Hester, Ariel I. Balter, Randy W. Heiland, Benjamin L. Zaitlen, James A. Glazier

      Pages 361-428

   4. BioLogic: A Mathematical Modeling Framework for Immunologists

      • Shlomo Ta’asan, Rima Gandlin

      Pages 429-443

   5. Dynamic Knowledge Representation Using Agent-Based Modeling: Ontology Instantiation and Verification of Conceptual Models

      • Gary An

      Pages 445-468

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.

• Biomedical research
• Biomolecular systems
• Cellular processes
• Large scale systems
• Spatial analysis
• Termination
• biology
• genome
• methodology
• molecular biology
• Systems Biology

From the reviews: “This volume considers systems biology in the broadest terms: the integration of experimental and mathematical approaches to biological systems with the aim of gaining both predictive and explanatory power. … the methods are clearly explained and well-illustrated … . Therefore, this volume will generally be of most value as an institutional purchase.” (Conrad Nieduszynski, Microbiology Today, January, 2010)

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