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In Silico Systems Biology

  • Book
  • © 2013

Overview

Editors:
  1. Maria Victoria Schneider

    1. The Genome Analysis Centre, Norwich, United Kingdom

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  • Includes cutting-edge methods and protocols in the MiMB standard format
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1021)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-x
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  2. Defining Systems Biology: A Brief Overview of the Term and Field

    • Maria Victoria Schneider
    Pages 1-11

  3. Approaches to Modeling Gene Regulatory Networks: A Gentle Introduction

    • Thomas Schlitt
    Pages 13-35

  4. Integration of Genomic Information with Biological Networks Using Cytoscape

    • Anna Bauer-Mehren
    Pages 37-61

  5. Visualization and Analysis of Biological Networks

    • Pablo Porras Millán
    Pages 63-88

  6. Modeling Signaling Networks with Different Formalisms: A Preview

    • Aidan MacNamara, David Henriques, Julio Saez-Rodriguez
    Pages 89-105

  7. From a Biological Hypothesis to the Construction of a Mathematical Model

    • David Cohen, Inna Kuperstein, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone
    Pages 107-125

  8. Practical Use of BiNoM: A Biological Network Manager Software

    • Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Zinovyev
    Pages 127-146

  9. Using Chemical Kinetics to Model Biochemical Pathways

    • Nicolas Le Novère, Lukas Endler
    Pages 147-167

  10. Simulation of Stochastic Kinetic Models

    • Andrew Golightly, Colin S. Gillespie
    Pages 169-187

  11. BioModels Database: A Repository of Mathematical Models of Biological Processes

    • Vijayalakshmi Chelliah, Camille Laibe, Nicolas Le Novère
    Pages 189-199

  12. Supporting SBML as a Model Exchange Format in Software Applications

    • Sarah M. Keating, Nicolas Le Novère
    Pages 201-225

  13. Controlled Annotations for Systems Biology

    • Nick Juty, Camille Laibe, Nicolas Le Novère
    Pages 227-245

  14. Bayesian Approaches for Mechanistic Ion Channel Modeling

    • Ben Calderhead, Michael Epstein, Lucia Sivilotti, Mark Girolami
    Pages 247-272

  15. Building Models Using Reactome Pathways as Templates

    • David Croft
    Pages 273-283

  16. Uniform Curation Protocol of Metazoan Signaling Pathways to Predict Novel Signaling Components

    • Máté Pálfy, Illés J. Farkas, Tibor Vellai, Tamás Korcsmáros
    Pages 285-297

  17. Bioinformatics Workflows and Web Services in Systems Biology Made Easy for Experimentalists

    • Rafael C. Jimenez, Manuel Corpas
    Pages 299-310

  18. Back Matter

    Pages 311-313
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Keywords

About this book

Systems biology can now be considered an established and fundamental field in life sciences. It has moved from the identification of molecular 'parts lists' for living organisms towards synthesising information from different 'omics'-based approaches to generate and test new hypotheses about how biological systems work. In In Silico Systems Biology: Methods and Protocols, expert researchers in the field detail a practical set of chapters based often on actual materials used and develop for face-to-face training with examples and case studies.  Written in the highly successful Methods in Molecular Biology  series format, chapters include introductions to their respective topics, step-by-step workflows, and key tips on troubleshooting and avoiding known pitfalls.

 Authoritative and practical, In Silico Systems Biology: Methods and Protocols seeks to aid scientists in the further study of network biology and mathematical models of biological systems.

Editors and Affiliations

  • The Genome Analysis Centre, Norwich, United Kingdom

    Maria Victoria Schneider

Bibliographic Information

  • Book Title: In Silico Systems Biology

  • Editors: Maria Victoria Schneider

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-450-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2013

  • Hardcover ISBN: 978-1-62703-449-4Published: 29 May 2013

  • Softcover ISBN: 978-1-4939-6295-2Published: 23 August 2016

  • eBook ISBN: 978-1-62703-450-0Published: 29 May 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 313

  • Number of Illustrations: 18 b/w illustrations, 70 illustrations in colour

  • Topics: Bioinformatics

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