3.2         Differences between Gene Net and Biopathway Modeling Modes

The differences between the Biopathway modeling mode and the Gene Net mode are listed in the table below.

 

 

Biopathway Modeling Mode

Gene Net Mode

Model

Includes 3 base elements: entity, process and connector.

Models are created by the user within CI workspace.

Biopathway models are smaller but more precisely defined than the Gene Network models.

Biopathway models include quantitative simulation properties for studying the kinetics of biological processes.

 

Includes 2 basic elements: gene and edge.

Gene networks are automatically generated by a special external software.

Originally gene networks are large models without precise simulation data. 

Visualization

More advanced graphics: images for each graph elements, polygon and curved edges for connectors, visualization and animation of simulation progress, etc.

Visualization is slower but allows for displaying more details.

 

Simple graphics: default view styles for each gene and edge.

Visualization is faster but includes less details. Thus it is more suitable for large networks.

Editing

Many commands enable building biopathway models from the scratch and defining the simulation properties (e.g. kinetic styles)

Extraction and Merging of subnetworks. Other edit commands are used in seldom cases.

Simulation

Simulation using Petri Net algorithm in interactive or remote mode.

no Simulation capabilities

Analysis

Analysis of simulation results: charts

Analysis of gene networks: Gene Mining, Pathway and Keyword Search, Expression Plot, tools for extraction of subnets