Opis

The developing methods of systems biology can help investigators to make inference and predictions from their data; 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. This work offers information on this field.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 Biology" 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: 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 Julius Parulek, Milos A ramek, Michal Cervenansku, Marta Novotova, and Ivan Zahradnik 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 Heterogeneous Experimental 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