Appendices #

It is desired to make the book as self-contained as possible; therefore, additional material in the form of five online appendices are also included.

A. Introduction to Key Biological Concepts #

This appendix provides a quick introduction to biology, focussing on basic biological macromolecules such as nucleic acids, proteins, carbohydrates, lipids, and small molecules. It also provides a brief overview of information flow in biological systems, discussing aspects of DNA replication, mRNA transcription, protein translation, and post-translational modifications.

B. Reconstruction of Biological Networks #

This appendix provides an overview of reconstruction of various types of biological networks, viz. gene regulatory networks, protein–protein interaction networks, signalling networks, and metabolic networks.

C. Databases for Systems Biology #

This appendix presents a brief overview of databases of PPIs and functional associations, metabolic network databases, gene regulatory network databases, model databases, and certain miscellaneous databases.

D. Software Tools Compendium #

Beginning with a summary of standards and formats, this appendix details various software tools that are useful for all the modelling paradigms studied in the book, such as network biology, dynamic modelling and parameter estimation, Boolean networks, constraint-based modelling, and community modelling.

E. MATLAB for Systems Biology #

This appendix provides a solid introduction to the basics of using MATLAB, followed by a discussion on how a variety of tools and toolboxes can be used for handling various modelling and simulation tasks in systems biology.

Appendices are located online-only at https://www.routledge.com/9781138597327.