The Helix research group
Research themes
Work in progress and results
Software and databases
News from Helix
Software and databases
Home page
Site map Mail to Helix
GEB: GenoExpertBacteria
Exploration of bacterial genomic, proteic and functional data

Turning genomic and post-genomic data into biological knowledge is a highly exploratory process. GEB has been designed to challenge this goal. GEB is a bioanalysis environment in which all the data are explicitly represented in a consistent way using a formal knowledge model.

GEB is composed of two parts:
-  GEB KB: the knowledge base
-  GEB browser: the user environment

-  GEB KB is built on an entity-relationship knowledge representation system (AROM). It represents explicitly information at the genomic level, at the protein level and at the functional level, with a special emphasis on intermediate metabolism (compounds, biochemical reactions, enzyme and metabolic pathways).

-  GEB browser is a Java application that allows to access, query and visualize objects of the GEB-KB.

The heterogeneous data (genomic, proteic, metabolic) represented in the KB are viewed as a wide information network. For each object, its properties as well as its relationships with the other objects of the KB are accessible. Hence, the GEB browser allows navigation through the information network and graphical visualisation using specialized tools:
-  a cartographic viewer for the genetic elements,
-  a pathway viewer for the metabolic pathways,
-  a biochemical reaction viewer,
-  a low MW compound viewer.

GEB is distributed by the Genostar company as PathwayExplorer, a module of its Iogma environment.

In the same section
The GenoStar integrated bioinformatics platform for exploratory genomics
GEB: GenoExpertBacteria
GNA: Genetic Network Analyzer
PepLine: high throughput proteomics
Herbs: checking the consistency of proteome annotations
ISee: In Silico biology e-learning environment
BOX: XML specifications of genomic data
AROM: entity-relationship knowledge modeling
    Top of page   Home page  Prepare to print