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The rapidly developing methods of systems biology can help investigators to make inference and predictions from their data that intuition alone would not discern; however, the difficulty lies in the broad knowledge of mathematics and engineering that seems to be required to even evaluate the applicability of the methods to the problem at hand.
In Systems Biology, scientists who possess that mathematical knowledge and have applied it effectively to various biological problems contribute methods which reflect their experience, crystallized in a form very similar to typical biological laboratory protocols. In order to best aid researchers, the chapters supply the theory behind the method, its step-by-step implementation, and the pitfalls explained thoroughly and from the practical angle. As a volume of the highly successful Methods in Molecular BiologyT series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.
Cutting-edge and easy to use, Systems Biology shatters the perceived insurmountable barrier between the laboratory and systems-biological research techniques.
Part I: Introduction1. Introduction: A Practical Guide to the Systems Approach in BiologyIvan V. Maly Part II: Methods for Analyzing Biomolecular Systems2. Computational Modeling of Biochemical Networks Using COPASIPedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada, and Ursula Kummer3. Flux Balance Analysis (FBA): Interrogating Genome-Scale Metabolic NetworksMatthew A. Oberhardt, Arvind K. Chavali, and Jason A. Papin4. Modeling Molecular Regulatory Networks with JigCell and PETClifford A. Shaffer, Jason W. Zwolak, Ranjit Randhawa, and John J. Tyson5. Rule-Based Modeling of Biochemical Systems with BioNetGenJames R. Faeder, Michael L. Blinov, and William S. Hlavacek6. Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory NetworksKerry J. Kim Part III: Spatial Analysis and Control of Cellular Processes7. Microfluidics Technology for Systems Biology ResearchC. Joanne Wang and Andre Levchenko8. Systems Approach to Therapeutics DesignBert J. Lao and Daniel T. Kamei9. Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell ModelsJacob Czech, Markus Dittrich, and Joel R. Stiles10. A Cell Architecture Modeling System Based on Quantitative Ultrastructural CharacteristicsJulius Parulek, MiloA A ramek, Michal Cervenansku, Marta Novotova, and Ivan Zahradnik11. Location Proteomics: Systematic Determination of Protein Subcellular LocationJustin Newberg, Juchang Hua, and Robert F. Murphy Part IV: Methods for Larger-Scale Systems Analysis12. Model-based Global Analysis of Heterogeneous Experimental Data Using gfitMikhail K. Levin, Manju M. Hingorani, Raquell M. Holmes, Smita S. Patel, and John H. Carson13. 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. Glazier14. BioLogic: A Mathematical Modeling Framework for ImmunologistsShlomo Ta'asan and Rima Gandlin15. Dynamic Knowledge Representation Using Agent Based Modeling: Ontology Instantiation and Verification of Conceptual ModelsGary An16. Systems Biology of Microbial CommunitiesAli Navid, Cheol-Min Ghim, Andrew T. Fenley, Sooyeon Yoon, Sungmin Lee, and Eivind Almaas
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)