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.

Part I: Introduction 1. Introduction: A Practical Guide to the Systems Approach in Biology Ivan V. Maly Part II: Methods for Analyzing Biomolecular Systems 2. Computational Modeling of Biochemical Networks Using COPASI Pedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada, and Ursula Kummer 3. Flux Balance Analysis (FBA): Interrogating Genome-Scale Metabolic Networks Matthew A. Oberhardt, Arvind K. Chavali, and Jason A. Papin 4. Modeling Molecular Regulatory Networks with JigCell and PET Clifford A. Shaffer, Jason W. Zwolak, Ranjit Randhawa, and John J. Tyson 5. Rule-Based Modeling of Biochemical Systems with BioNetGen James R. Faeder, Michael L. Blinov, and William S. Hlavacek 6. Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks Kerry J. Kim Part III: Spatial Analysis and Control of Cellular Processes 7. Microfluidics Technology for Systems Biology Research C. Joanne Wang and Andre Levchenko 8. Systems Approach to Therapeutics Design Bert J. Lao and Daniel T. Kamei 9. Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models Jacob Czech, Markus Dittrich, and Joel R. Stiles 10. A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics Július Parulek, Miloš Šrámek, Michal Cervenanský, Marta Novotová, and Ivan Zahradník 11. Location Proteomics: Systematic Determination of Protein Subcellular Location Justin Newberg, Juchang Hua, and Robert F. Murphy Part IV: Methods for Larger-Scale Systems Analysis 12. Model-based Global Analysis of HeterogeneousExperimental Data Using gfit Mikhail K. Levin, Manju M. Hingorani, Raquell M. Holmes, Smita S. Patel, and John H. Carson 13. Multi-Cell 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, and James A. Glazier 14. BioLogic: A Mathematical Modeling Framework for Immunologists Shlomo Ta’asan and Rima Gandlin 15. Dynamic Knowledge Representation Using Agent Based Modeling: Ontology Instantiation and Verification of Conceptual Models Gary An 16. Systems Biology of Microbial Communities Ali Navid, Cheol-Min Ghim, Andrew T. Fenley, Sooyeon Yoon, Sungmin Lee, and Eivind Almaas