GINsim 3.0 Documentation

GINsim (see Naldi 2009) is a tool implementing the multilevel logical formalism. It leans on two main types of graphs: Logical Regulatory Graphs, which model regulatory networks, and State Transition Graphs, which represent their dynamical behaviour. See also the Tutorial.

Introduction — Motivation and concepts
Install and Run GINsim — Availability, requirements, first run

Define Logical Regulatory Graphs

Annotations — Annotate regulatory graph elements
Compute interaction functionality — Compute interaction functionality
Logical Regulatory Graphs — Graphs defining logical models
Editing the regulatory graph — Edit logical regulatory graphs
Dynamical behaviour — Define the dynamical rules: parameters and functions

Modify Logical Regulatory Graphs

Booleanization of regulatory graphs — Boolean mapping for multivalued models
Composition of LRGs — Composing multiple instances of an LRG, indicating logical integration functions mapping selected input components to proper components in neighbouring instances
Reduction of regulatory graphs — Removing components from a LRG, preserving dynamical properties
Reversal of regulatory graphs — Compute a LRG generating the reversed asynchronous dynamics
Perturbations — Define perturbations of regulatory graphs

Simulation and Transition Graphs

Initial states — Define initial states for regulatory graph
Transition Graphs — Detailled representation of the dynamical behaviour
The simulation — Generate Transition Graphs
Updating mode — Updating mode for the simulation

Analyse Transition Graphs

Animator for the State Transition Graphs — Animate the model based on its dynamics
Extract STG from HTG — Build the STG underlying parts of a HTG
HTG Edge Analysis — Analyse edges in a HTG
Strongly Connected Components — Compute the Strongly Connected Components Graph

Static Analysis of Logical Regulatory Graphs

Circuit analysis — Lookup the Functionality of Regulatory Circuits
Highlight local graph — Highlight the local graph
Stable state search — Finding stable states for a regulatory graph
Trapspace search — Finding trapspaces of a regulatory graph

Generic Graphs

GINsim relies on Graphs to represent logical models and their dynamical behaviour.

Find node — Search for nodes in LRGs and STGs
Find path — Define and search for paths in LRGs and STGs
Graph layouts — Automatic positionning of graph elements
Graph selection — Handle the selected items in a graph
Strongly Connected Components — Compute the Strongly Connected Components Graph
Styling graphs — Edit visual style

Graphical User Interface

Graph view — Editing the graph view
Processing a new graph — What to do with a new graph
The main window — View and edit graphs, launch actions
Welcome dialog — The welcome dialog

Save, Export, Import

Documentation export — Generate LRG documentation using annotations
Export graph structure — Export the structure of a graph
Export graph view — Export graph view as image
Export to other logical modelling tools — Import/Export regulatory graphs
The Z-GINML format — The native file format in GINsim

Going Further

Scripting GINsim — Scripting GINsim
Troubleshooting — Debug problems