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The GenoStar integrated bioinformatics platform for exploratory genomics
Developed by the Genostar consortium

The name "GenoStar" was given originally to the integrated bioinformatics environment developed by a consortium of four members: INRIA, Institut Pasteur, Hybrigenics and GENOME express. The consortium was partly supported by the French Ministry for Research (Programme Génomique and Programme GenHomme).

The GenoStar bioinformatics environment was made up of several application modules which shared data and knowledge management facilities. All the data manipulated by the application modules, and all the results they produce, are explicitly represented in an entity-relationship model: AROM. Within a module, methods are organized into strategies, the execution of which adresses complex analysis problems.

The final version of GenoStar developped by the consortium, version 2.0, was made up of three application modules: GenoAnnot, GenoLink and GenoBool which easily exchanged data.

GenoAnnot relied on several sequence analysis methods to perform the syntactic annotation of bacterial genomes. It produced predictions on the position of genes and other pertinent features. Conflicting and convergent predictions were displayed with the help of a map viewer. GenoAnnot was extended to the annotation of eukaryotic genomes.

GenoLink was designed to allow biologists to browse through a network of biological entities and bioinformatics objects, to help them to understand the function of genes. The links of a network represent different relationships between the entities and the set of their type is easily extendable. For instance, two genes may be connected because of their sequence similarity, but also because their products are involved in the same metabolic pathway, or because the proteins they code for exhibit the same isoelectric point. A powerful request engine allowed exploration of the network to draw meaningful inferences.

GenoBool offered several data analysis methods to be applied to heterogeneous sets of data after they have been adequately coded, for example using Boolean coders. GenoBool thus allowed the user to discover new relationships between properties of biological entities. Once the pertinence of a relationship was asserted, it could lead to the introduction of a new kind of link in GenoLink.

However, the attractiveness of GenoStar for genomic data analysis extended far beyond the capabilities of these three modules. Its very architecture offered several original features to help the biologist to apply complex and exploratory analysis tasks.

The first version of GenoStar 1.1 was released in December 2002.

Version 1.2 was released in June 2003 to more than 50 French research groups. Version 2.0 was released in December 2003.

In 2005, the rights to further develop and to distribute the GenoStar bioinformatics software were granted to the Genostar company.

Genostar has further developed the capabilities and functions of the integrated environment and renamed it IOGMA.

How to get GenoStar 2.0 ?

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
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