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Systems Biology

  • Book
  • © 2009

Overview

Editors:
  1. Ivan V. Maly
    View editor publications

    You can also search for this editor in 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)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. Introduction: A Practical Guide to the Systems Approach in Biology

      • Ivan V. Maly
      Pages 1-11

  3. Methods for Analyzing Biomolecular Systems

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Computational Modeling of Biochemical Networks Using COPASI

      • Pedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada, Ursula Kummer
      Pages 17-59

    3. Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks

      • Matthew A. Oberhardt, Arvind K. Chavali, Jason A. Papin
      Pages 61-80

    4. Modeling Molecular Regulatory Networks with JigCell and PET

      • Clifford A. Shaffer, Jason W. Zwolak, Ranjit Randhawa, John J. Tyson
      Pages 81-111

    5. Rule-Based Modeling of Biochemical Systems with BioNetGen

      • James R. Faeder, Michael L. Blinov, William S. Hlavacek
      Pages 113-167

    6. Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks

      • Kerry J. Kim
      Pages 169-200

  4. Spatial Analysis and Control of Cellular Processes

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Microfluidics Technology for Systems Biology Research

      • C. Joanne Wang, Andre Levchenko
      Pages 203-219

    3. Systems Approach to Therapeutics Design

      • Bert J. Lao, Daniel T. Kamei
      Pages 221-236

    4. Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models

      • Jacob Czech, Markus Dittrich, Joel R. Stiles
      Pages 237-287

    5. A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics

      • Július Parulek, Miloš Šrámek, Michal Červęanský, Marta Novotová, Ivan Zahradník*
      Pages 289-312

    6. Location Proteomics: Systematic Determination of Protein Subcellular Location

      • Justin Newberg, Juchang Hua, Robert F. Murphy
      Pages 313-332

  5. Methods for Larger-Scale Systems Analysis

    1. Front Matter

      Pages 1-1
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    2. Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit

      • Mikhail K. Levin, Manju M. Hingorani, Raquell M. Holmes, Smita S. Patel, John H. Carson
      Pages 335-359

    3. Multicell 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 361-428

    4. BioLogic: A Mathematical Modeling Framework for Immunologists

      • Shlomo Ta’asan, Rima Gandlin
      Pages 429-443

    5. Dynamic Knowledge Representation Using Agent-Based Modeling: Ontology Instantiation and Verification of Conceptual Models

      • Gary An
      Pages 445-468
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Keywords

About this book

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.

Reviews

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)

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

  • Industry Sectors: Biotechnology

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