Preface ; List of authors ; Part I: Molecular level ; 1. Selected aspects of biological network analysis ; 1.1 Introduction ; 1.2 Selected biological databases ; 1.2.1 Case study: Gene Expression Omnibus ; 1.2.2 RegulonDB ; 1.3 Types of biological networks
1.3.1 Relations between molecules and types of networks 1.3.2 Biochemical pathways ; 1.4 Network development models ; 1.4.1 Selected tools for assembling networks on the basis of gene expression data ; 1.4.2 Selected tools for reconstruction of networks via literature mining
1.5 Network analysis 1.5.1 Selected tools ; 1.5.2 Cytoscape analysis examples ; 1.6 Summary ; Part II: Cellular level ; 2. Negative feedback inhibition -- Fundamental biological regulation in cells and organisms ; 2.1 Negative feedback-based systems simulations ; 2.1.1 Introduction
2.1.2 Glossary of Terms 2.1.3 Software model ; 2.1.4 Application manual ; 2.1.5 OS model example ; 2.1.6 Simulation algorithm ; 3. Information -- A tool to interpret the biological phenomena ; Part III: Organ level ; 4. The virtual heart
5. Modeling figure/ground separation with spiking neurons 5.1 Introduction ; 5.2 Figure/ground separation ; 5.3 Spiking neural networks ; 5.4 Lateral connections via gap junctions ; 5.5 Simulation of a sheet of laterally connected neurons ; 5.6 Basis of our model ; 5.7 Conclusion
Summary
This book describes biological and medical phenomena and how they can be virtually simulated by breaking them down into basic principles. It introduces a wide spectrum of applications, from molecules, tissues, and organs up to the whole body, with a focus on how to use and interpret these simulations. The book is complemented by topics such as serious games and distance medicine
