Systems Biology

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 CharacteristicsJúlius Parulek, Milos Srámek, Michal Cervenanský, Marta Novotová, and Ivan Zahradník11. 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 HeterogeneousExperimental 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