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Life Sciences - Systems Biology and Bioinformatics | In Silico Systems Biology

In Silico Systems Biology

Series: Methods in Molecular Biology, Vol. 1021

Schneider, Maria Victoria (Ed.)

2013, X, 313 p. 88 illus., 70 illus. in color.

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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

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

Content Level » Professional/practitioner

Keywords » 'omics'-based approaches - Silico Systems - biological data - handling and annotating networks - mathematical models - molecular 'parts lists' for living organisms - network biology - systems biology

Related subjects » Systems Biology and Bioinformatics

Table of contents 

1. Defining Systems Biology: A Brief Overview of the Term and Field

Maria Victoria Schneider

 2. Approaches to Modelling Gene Regulatory Networks - A Gentle Introduction

Thomas Schlitt

3. Integration of Genomic Information with Biological Networks using Cytoscape

Anna Bauer-Menren

4. Visualization and Analysis of Biological Networks

Pablo Porras Millán

 5. Modeling Signaling Networks with Different Formalisms:  A Preview

Aidan MacNamara, David Henriques, and Julio Saez-Rodriguez

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

David Cohen, Inna Kuperstein, Emmanuel Barillot, Andrei Zinovyev and Laurence Calzone

 7. Practical use of BiNoM, a Biological Network Manager Software

Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, and Andrei Zinovyev

 8. Using Chemical Kinetics to Model Biochemical Pathways

Nicolas Le Novère and Lukas Endler

 9. Simulation of Stochastic Kinetic


Andrew Golightly and Colin S. Gillespie

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

Vijayalakshmi Chelliah, Camille Laibe, and Nicolas Le Novère

11. Supporting SBML as a Model Exchange Format in Software


Sarah M. Keating and Nicolas Le Novere

 12. Controlled Annotations for Systems Biology

Nick Juty, Camille Laibe, and Nicolas Le Novère

 13. Bayesian Approaches for Mechanistic

Ion Channel Modelling

Ben Calderhead, Michael Epstein, Lucia Sivilotti, Mark Girolami

14. Building Models using Reactome Pathways as Templates

David Croft

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

Máté Pálfy, Illés J. Farkas, Tibor Vellai, and  Tamás Korcsmáros

16. Bioinformatics Workflows and Web-services in Systems Biology Made Easy for Experimentalists

Rafael C. Jimenez and Manuel Corpas

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