Overview
- Editors:
- Ivan V. Maly
Search author on:PubMed Google Scholar
- Written by leading scientists who apply quantitative systems methodology in their biological research
- Covers a broad range of methods with a proven record of application to a wide variety of biomedical research problems
- Step-by-step instructions for implementing computational techniques, much like in a laboratory protocol
- Addresses the caveats of applying the systems analysis to biology from the practical researcher's standpoint
- Uniquely broad coverage of quantitative methods that account for the complex structural organization in biological systems
- Includes supplementary material:sn.pub/extras
Part of the book series:Methods in Molecular Biology (MIMB, volume 500)
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Table of contents (16 protocols)
Front Matter
Pages i-xiIntroduction
Front Matter
Pages 1-1
Methods for Analyzing Biomolecular Systems
Front Matter
Pages 1-1Computational Modeling of Biochemical Networks Using COPASI
- Pedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada, Ursula Kummer
Pages 17-59Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks
- Matthew A. Oberhardt, Arvind K. Chavali, Jason A. Papin
Pages 61-80Modeling Molecular Regulatory Networks with JigCell and PET
- Clifford A. Shaffer, Jason W. Zwolak, Ranjit Randhawa, John J. Tyson
Pages 81-111Rule-Based Modeling of Biochemical Systems with BioNetGen
- James R. Faeder, Michael L. Blinov, William S. Hlavacek
Pages 113-167Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks
- Kerry J. Kim
Pages 169-200
Spatial Analysis and Control of Cellular Processes
Front Matter
Pages 1-1Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models
- Jacob Czech, Markus Dittrich, Joel R. Stiles
Pages 237-287A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics
- Július Parulek, Miloš Šrámek, Michal Červęanský, Marta Novotová, Ivan Zahradník*
Pages 289-312Location Proteomics: Systematic Determination of Protein Subcellular Location
- Justin Newberg, Juchang Hua, Robert F. Murphy
Pages 313-332
Methods for Larger-Scale Systems Analysis
Front Matter
Pages 1-1Model-Based Global Analysis of Heterogeneous Experimental Data Usinggfit
- Mikhail K. Levin, Manju M. Hingorani, Raquell M. Holmes, Smita S. Patel, John H. Carson
Pages 335-359Multicell 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 361-428BioLogic: A Mathematical Modeling Framework for Immunologists
- Shlomo Ta’asan, Rima Gandlin
Pages 429-443
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Bibliographic Information
Book Title:Systems Biology
Editors:Ivan V. Maly
Series Title:Methods in Molecular Biology
DOI:https://doi.org/10.1007/978-1-59745-525-1
Publisher:Humana Totowa, NJ
eBook Packages:Springer Protocols
Copyright Information:Humana Press 2009
Hardcover ISBN:978-1-934115-64-0Published: 26 March 2009
Softcover ISBN:978-1-62703-949-9Published: 27 November 2014
eBook ISBN:978-1-59745-525-1Published: 29 April 2009
Series ISSN: 1064-3745
Series E-ISSN: 1940-6029
Edition Number:1
Number of Pages:XI, 500
Topics:Bioinformatics,Systems Biology,Computer Appl. in Life Sciences