Chapters
Chapter 01: Graph Theory for Systems Biology: Interval graphs, motifs, and patterns recognition
John R. Jungck and Rama Viswanathan
- Chapter 1 Figures (PPT)
- Ch01_BioGrapher_Tutorial(PDF)
- Ch01_examples_data(zip file)
- Guidelines for Projects (PDF)
Chapter 02: Food Webs and Graphs
Margaret (Midge) Cozzens
Chapter 03: Adaptation and Fitness Graphs
Kristina Crona and Emilie Wiesner
Chapter 04: Signaling Networks: Asynchronous Boolean models
Réka Albert and Raina Robeva
Chapter 05: Dynamics of Complex Boolean Networks: Canalization, stability, and criticality
Qijun He, Matthew Macauley and Robin Davies
Chapter 06: Steady State Analysis of Boolean Models: A dimension reduction approach
Alan Veliz-Cuba and David Murrugarra
Chapter 07: BioModel Engineering with Petri Nets
Mary Ann Blätke, Monika Heiner and Wolfgang Marwan
- Chapter 7 Figures (PPT)
- Code_for_chapter07_examples(zip file)
- Code_for_chapter07_exercise_solutions(zip file)
- Solutions to Exercises(PDF)
Chapter 08: Transmission of Infectious Diseases: Data, models, and simulations
Winfried Just, Hannah Callender, M. Drew LaMar and Natalia Toporikova
- Chapter 8 Figures (PPT)
- Solutions to Exercises(PDF)
- Chapter_08_IONTWv1.1(zip file)
- Online Appendix(PDF)
Chapter 09: Disease Transmission Dynamics on Networks: Network structure versus disease dynamics
Winfried Just, Hannah Callender and M. Drew LaMar
- Chapter 9 Figures (PPT)
- Chapter_09_IONTWv1.1(zip file)
- Solutions to Exercises(PDF)
- Online Appendix(PDF)
Chapter 10: Predicting Correlated Responses in Quantitative Traits Under Selection: A linear algebra approach
Janet Steven and Bessie Kirkwood
Chapter 11: Metabolic Analysis: Algebraic and geometric methods
Terrell L. Hodge, Blair R. Szymczyna and Todd J. Barkman
- Chapter 11 Figures (PPT)
- Solutions to Exercises(PDF)
- Online Appendix(PDF)
- Ch11_Resources (Chapter11__resources.zip)
Chapter 12: Reconstructing the Phylogeny: Computational methods
Grady Weyenberg and Ruriko Yoshida
Chapter 13: RNA Secondary Structures: Combinatorial models and folding algorithms
Qijun He, Matthew Macauley and Robin Davies
Chapter 14: RNA Secondary Structures: An approach through pseudoknots and fatgraphs
Christian M. Reidys