3 August 2009
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. Collecting information on 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
2.3. 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.
File
menu
2.8.2.
Edit
menu
2.8.3.
Analysis
menu
2.8.4.
Results
menu
2.8.5.
Windows
menu
2.8.6.
Help
menu
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
List of Figures
2.1.
Schema of genetic regulatory network
2.2.
Project and Influence graph windows
2.3.
Variable
window after creation of the parameters
2.4.
Variable
window after definition of the state equation
2.5.
Variable
window after definition of the inequality constraints
2.6.
Initial conditions
window
2.7.
Simulation
window
2.8.
Simulation results
2.9.
Simulation results: fragment of the state transition graph
2.10.
Qualitative evolution of the variables
2.11.
Attractor search
window
2.12.
Atomic proposition
windows
2.13.
Pattern
wizard of the property editor
2.14.
Expert
tab of the property editor
2.15.
Verification
window
2.16.
Menu of the graphical user interface
Next
Part 1. Overview of GNA
