BookPablo Carbonell.
Summary: This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master's students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.
Contents:
Part I. Metabolic Pathway Modeling
Getting on the Path to Engineering Biology
Genome-Scale Modeling
Pathway Modeling
Modeling Chemical Diversity
Part II. Metabolic Pathway Discovery
Enzyme Discovery and Selection
Pathway Discovery
Pathway Selection
Part III. Metabolic Pathway Design
Pathway Design
Pathway Redesign.