Mathematica v7 Workbooks from SYSTEMS BIOLOGY: Simulation of Dynamic Network States

PART I: Simulation of Dynamic States

Please put GraphDirectives.m into the same folder as the notebooks (or at a place where Mathematica can find it; check the $Path variable).

Chapter 3

Section 3.4 Section 3.4 Section 3.4 v2

Chapter 4

Section 4.2 Section 4.2 Section 4.2 v2

Section 4.3 Section 4.3 Section 4.3 v2

Section 4.4 Section 4.4 Section 4.4 v2

Section 4.5 Section 4.5 Section 4.5 v2

Section 4.5 Pools Section 4.5pools Section 3.4 v2

Chapter 5:

Section 5.3 Section 5.3 Section 5.3 v2

Section 5.4 Section 5.4 Section 5.4 v2

Section 5.5 Section 5.5 Section 5.5 v2

Chapter 6

Section 6.2 Section 6.2 Section 6.2 v2

Section 6.3 Section 6.3 Section 6.3 v2

PART II: Biological Characteristics

Chapter 7

Chapter 8

Section 8.3.1 Section 8.3.1 Section 8.3.1 v2

Section 8.3.2 Section 8.3.2 Section 8.3.2 v2

Section 8.3.3 Section 8.3.3 Section 8.3.3 v2

Section 8.4 Section 8.4 Section 8.4 v2

Chapter 9

Section 9.5 Section 9.5 Section 9.5 v2

Section 9.6.1 Section 9.6.1 Section 9.6.1 v2

Section 9.6.2 Section 9.6.2 Section 9.6.2 v2

PART III: Metabolism

Functions.m file (required for use of Chapter 10-14 workbooks) functions.m

Chapter 10 Glycolysis Simulator

Chapter 11 Glycolysis PPP Simulator

Chapter 12 Glycolysis PPP AMP Salvage Simulator

PART IV: Simulation of Macromolecular Systems

Chapter 13 Hemoglobin Simulator Glycolysis Hemoglobin Simulator

Chapter 14 PFK steady state solution Glycolysis PFK Simulator