8 March 2010

Genetic Network Analyzer Tutorial

Table of Contents

1. Overview of GNA

1.1. What is GNA?
1.2. Projects using GNA

2. Using GNA

2.1. Defining a network

2.1.1. Define simple genetic regulatory network
2.1.2. Define more complex regulatory networks
2.1.3. Reduction of regulatory network

2.2. Building a model

2.2.1. Definition of state and input variables
2.2.2. Definition of parameters
2.2.3. Definition of state equations
2.2.4. Definition of inequality constraints
2.2.5. Definition of the model through wizard

2.3. Specifying initial conditions

2.4. Running simulations

2.5. Interpreting simulation results

2.6. Searching for attractors

2.7. Checking properties of the state transition graph

2.7.1. Specification of atomic propositions
2.7.2. Formulation of temporal logic formulas
2.7.3. Verification of temporal logic formulas

2.8. Functions of the graphical user interface

2.8.1. Network editor
2.8.2. Model editor

3. Appendices

3.1. Syntax of GNA model

3.1.1. Syntactic conventions
3.1.2. BNF of a model
3.1.3. Additional constraints

3.2. Syntax of GNA initial conditions

3.2.1. Syntactic conventions
3.2.2. BNF of an initial conditions file
3.2.3. Additional constraints

3.3. Syntax of CTRL property

3.3.1. Syntactic conventions
3.3.2. BNF of a property
3.3.3. Additional constraints
3.3.4. BNF of a property formula

3.4. CUP Parser Generator license

3.5. JGraph license

3.6. SAT4J license

3.7. NuSMV license

List of Figures

2.1. Schema of simple genetic regulatory network
2.2. Schema of a more complex genetic regulatory network
2.3. Schema of reduced genetic regulatory network
2.4. Reduced network window
2.5. Variable window after creation of the parameters
2.6. Variable window after definition of the state equation
2.7. Variable window after definition of the inequality constraints
2.8. Wizard window for the definition of variables
2.9. Wizard window for the definition of state equation
2.10. Initial conditions window
2.11. Simulation window
2.12. Simulation results
2.13. Simulation results: fragment of the state transition graph
2.14. Qualitative evolution of the variables
2.15. Attractor search window
2.16. Atomic proposition windows
2.17. Pattern wizard of the property editor
2.18. Expert tab of the property editor
2.19. Verification window
2.20. Menu of the graphical user interface (network editor)
2.21. Menu of the graphical user interface (model editor)

Part 1. Overview of GNA