Book Volume 500 2009

Systems Biology

Editors:

ISBN: 978-1-934115-64-0 (Print) 978-1-59745-525-1 (Online)

Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi

  2. Introduction

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 1-11

      Introduction: A Practical Guide to the Systems Approach in Biology

  3. Methods for Analyzing Biomolecular Systems

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 17-59

      Computational Modeling of Biochemical Networks Using COPASI

    3. No Access

      Protocol

      Pages 61-80

      Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks

    4. No Access

      Protocol

      Pages 81-111

      Modeling Molecular Regulatory Networks with JigCell and PET

    5. No Access

      Protocol

      Pages 113-167

      Rule-Based Modeling of Biochemical Systems with BioNetGen

    6. No Access

      Protocol

      Pages 169-200

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

  4. Spatial Analysis and Control of Cellular Processes

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 203-219

      Microfluidics Technology for Systems Biology Research

    3. No Access

      Protocol

      Pages 221-236

      Systems Approach to Therapeutics Design

    4. No Access

      Protocol

      Pages 237-287

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

    5. No Access

      Protocol

      Pages 289-312

      A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics

    6. No Access

      Protocol

      Pages 313-332

      Location Proteomics: Systematic Determination of Protein Subcellular Location

  5. Methods for Larger-Scale Systems Analysis

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 335-359

      Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit

    3. No Access

      Protocol

      Pages 361-428

      Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment

    4. No Access

      Protocol

      Pages 429-443

      BioLogic: A Mathematical Modeling Framework for Immunologists

    5. No Access

      Protocol

      Pages 445-468

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

    6. No Access

      Protocol

      Pages 469-494

      Systems Biology of Microbial Communities

  6. Back Matter

    Pages 495-500