The differences between the Biopathway modeling mode and the Gene network mode are listed in the table below.
|
Biopathway Modeling Mode |
Gene Network 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 |