In Silico Systems Biology

This Methods in Molecular Biology(TM) book offers detailed coverage of current techniques in network biology and mathematical models of biological systems. Includes step-by-step workflows, as well as key tips on troubleshooting and avoiding known pitfalls.

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.

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

Inhalt

Defining Systems Biology: A Brief Overview of the Term and Field.- Approaches to Modelling Gene Regulatory Networks - A Gentle Introduction.- Integration of Genomic Information with Biological Networks using Cytoscape.- Visualization and Analysis of Biological Networks.- Modeling Signaling Networks with Different Formalisms: A Preview.- From a Biological Hypothesis to the Construction of a Mathematical Model.- Practical use of BiNoM, a Biological Network Manager Software.- Using Chemical Kinetics to Model Biochemical Pathways.- Simulation of Stochastic KineticModels.- BioModels Database: A Repository of Mathematical Models of Biological Processes.- Supporting SBML as a Model Exchange Format in Software Applications.- Controlled Annotations for Systems Biology.- Bayesian Approaches for Mechanistic Ion Channel Modelling.- Building Models using Reactome Pathways as Templates.- Uniform Curation Protocol of Metazoan Signaling Pathways to Predict Novel Signaling Components.- Bioinformatics Workflows and Web-services in Systems Biology Made Easy for Experimentalists.