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Three IBENS bioinformatic tools selected to be part of the European Elixir infrastructure

26 Bioinformatics tools selected in France to be part of the European Elixir infrastructure, 3 are developed and maintained at IBENS

GINsim & RSAT | M. Thomas Chollier & D. Thieffry
Genomicus | A. Louis & H. Roest Crollius

Elixir is the european infrastructure for bioinformatics. It provides a catalog of key resources selected by each country.
In 2019, The French Elixir node has labelled 26 bioinformatic tools or services after an extended reviewing process.

The eligibility was based on :
❑ Impact on French and international communities of research in life sciences
❑ Compliance to ELIXIR recommended good practices
❑ Sustainability

Three services developed and maintained at IBENS have been labellised.
This selection underlines the importance of these tools for the french and international community. It attests that they are developed according to the Elixir recommendations
ensuring large accessibility, major interest, and open science initiative. They are long-term and reliable resources for research community.

Genomicus (équipe Dyogen)
Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions : linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales : local gene order, karyotypes, matrix plots, etc.
Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.

GinSIM (équipe CSB)
GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.
Using its user-friendly graphical interface, users can specify a signed regulatory graph, define boolean or multivalued logical functions, and then simulate and analyse its
qualitative dynamical behaviour.

RSAT (équipe CSB)
Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities.
The tools can be accessed via a Web site (, as Web services, or installed locally on Linux / Mac OS X systems.

GINsim & RSAT : M. Thomas Chollier & D. Thieffry
Genomicus : A. Louis & H. Roest Crollius