Posts Tagged Software

GenOuest

Posted on décembre 6, 2009 by Commentaires fermés sur GenOuest

Logo_BioInfoGenouest

GenOuest is a bioinformatics platform hosted by INRIA Rennes Bretagne-Atlantique center and IRISA. This platform acted primarily as a core facility and software tool provider for the analysis of genomic data generated by the different laboratories of Biogenouest (formerly OUEST-genopole®). The plate-forme is IBiSA labelled since 2009.

The platform provides a complete bioinformatics environment: computing power, storage, databanks and also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. This activity results from a tight interaction between the GenOuest platform and the Symbiose research team (INRIA).

Among its activities GenOuest is involved in many development projects: user-oriented tools or technological transfer of new algorithms elaborated by Symbiose.
The platform is a member of the GRISBI platform, a joined project between six French bioinformatics platform aiming at the deployment of a bioinformatics grid. GenOuest is also a member of the MobyleNet project.

GenOuest is also providing a complete cursus of bioinformatics training: tools, methodologies, programming languages.

The platform is ISO9001:2000 certified since may 2008.

Outline :

People :

8 persons (2 on a permanent position)

Computer resources

2 clusters (200 cores) / 50 Tb storage

Hosted databases and specific public resources

  • Germonline
  • Mimas
  • Aphidbase
  • Autograph
  • Phymycodb
  • Rasta bacteria

Specific software

  • Stan
  • Wapam
  • Pygram
  • Logol
  • Protomata
  • Plast
  • iThos

Projects

  • GRISBI
  • MobyleNet
  • BioWIC

Training

The whole list of courses is available  here



Web site  : GenOuest

Logo_BioInfoGenouest

GenOuest is a bioinformatics platform hosted by INRIA Rennes Bretagne-Atlantique center and IRISA. This platform acted primarily as a core facility and software tool provider for the analysis of genomic data generated by the different laboratories of Biogenouest (formerly OUEST-genopole®). The plate-forme is IBiSA labelled since 2009.

The platform provides a complete bioinformatics environment: computing power, storage, databanks and also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. This activity results from a tight interaction between the GenOuest platform and the Symbiose research team (INRIA).

Among its activities GenOuest is involved in many development projects: user-oriented tools or technological transfer of new algorithms elaborated by Symbiose.
The platform is a member of the GRISBI platform, a joined project between six French bioinformatics platform aiming at the deployment of a bioinformatics grid. GenOuest is also a member of the MobyleNet project.

GenOuest is also providing a complete cursus of bioinformatics training: tools, methodologies, programming languages.

The platform is ISO9001:2000 certified since may 2008.

Outline :

People :

8 persons (2 on a permanent position)

Computer resources

2 clusters (200 cores) / 50 Tb storage

Hosted databases and specific public resources

  • Germonline
  • Mimas
  • Aphidbase
  • Autograph
  • Phymycodb
  • Rasta bacteria

Specific software

  • Stan
  • Wapam
  • Pygram
  • Logol
  • Protomata
  • Plast
  • iThos

Projects

  • GRISBI
  • MobyleNet
  • BioWIC

Training

The whole list of courses is available  here



Web site  : GenOuest

CBIB Bordeaux

Posted on décembre 6, 2009 by Commentaires fermés sur CBIB Bordeaux

Le Centre de Bioinformatique de Bordeaux (CBIB) a pour vocation de fédérer et de stimuler les projets de recherche en bioinformatique, de satisfaire les besoins bioinformatiques liés aux activités de recherche des laboratoires de biologie de la région et d’être un centre de ressources ouvert à l’ensemble de la communauté par la mise à disposition de services en accès public via le WEB.

La recherche en bioinformatique du CBiB se développe autour de deux axes :

  • l’application à la biologie de travaux de recherche en informatique menés au Laboratoire Bordelais de Recherche en Informatique (LaBRI) de l’Université Bordeaux 1,
  • le développement de nouvelles méthodes et de nouveaux outils pour exploiter les données de génomique et de génomique fonctionnelle.

Pour satisfaire les besoins des laboratoire de biologie, le CBIB :

  • assure la mise à disposition et la maintenance de ressources publiques (bases de données, programmes…) sur son centre de calcul,
  • offre un support (accueil, assistance et formation) aux utilisateurs de ces ressources,
  • réalise des prestations « à façon » dans le cadre de collaborations scientifiques autour de projets de recherche portés par des laboratoires de biologie.

Enfin, le CBiB s’efforce de rendre accessible à travers son site WEB l’ensemble des ressources (bases de données, programmes) déployées : qu’il s’agisse de ressources publiques installées sur les machines du CBiB ou de ressources développées au sein même du CBiB.



Site web : CBIB

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Filed Under: Sites

Sequence analysis tools

Posted on décembre 6, 2009 by Commentaires fermés sur Sequence analysis tools

Next-generation sequencing

MICSA A software for detecting transcription factor binding sites from NGS ChIPseq data
SVdetect A software for detecting structural rearrangements from NGS mate-pair genomic sequencing data
NG6 Storage and basic analysis of data produced by the 454 sequencer of the Sequencing and Genotyping platform
S-Mart Analysis tools box for high throughput management data: sequences produced by NGS technologies; for example, it manages RNA-Seq and ChIp-Seq data and provide many plots to visualize the data

Genome annotation

CAAT-Box Software package containing methods for the follow-up of the assembly phases and for initiating annotation during the finishing stage
MicroScope/MaGe (Re)annotation and comparative analysis of microbial genomes
Rasta-Bacteria Rapid Automated Scan for Toxins and Antitoxins in Bacteria
AGMIAL Integrated system for bacterial genome annotation

Genome visualisation

SynteBase/SynteView A tool to visualize gene order conservation in prokaryotic genomes
Autograph Interactive web server for automating and visualizing comparative genome maps
MuGeN Software package for the visual exploration of multiple annotated genome portions

DNA & Protein motifs

Dr Motifs A comprehensive portal for pattern matching and discovery.
STAN Nucleic or proteic pattern search based on SVG (String Variable Grammar)
CRISPI User-friendly web interface with many graphical tools and facilities allows extracting CRISPR, finding out CRISPR in personal sequences or calculating sequence similarity with spacers
ModuleOrganizer Detecting modules in families of transposable elements
Hectar Heterokont subcellular targeting prediction (ABiMS resource)
R’MES Finding exceptional motifs in sequences
PRIAM Enzyme-specific profiles for metabolic annotation
REPET Analysis tool for detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs)
BLASTER Analysis suite for transposable element search and annotation in large eukaryotic genome sequence but generic enough to be applied in other contexts

RNA

VARNA Interactive drawing and editing of the RNA secondary structure
Erpin A program for the detection of RNA motifs inferred from RNA sequence alignments
RNAspace Integrated environment for non-coding RNA annotation; RNAspace makes available a variety of ncRNA gene finders and ncRNA databases as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs

Phylogeny

PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
TreeDyn Dynamic graphics and annotations for analyses of trees
GenePop Population genetics software package
APE Analyses of phylogenetics and evolution in R language
MLVA web service Databases of tandem repeats typing data for population studies of bacterial pathogens; tools to produce additional private or public databases
Phylogeny.fr Automated and configurable workflow for molecular phylogeny
SeaView Multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny

Miscellaneous

GenRGenS Software for generating random genomic sequences and structures
genofrag/iThos Tool for segmenting bacterial genomes into fragments of identical size for long-range PCR amplification
Gigablaster Fast parallel Blast search on specialized sequence databases
Tcoffee A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures
ADE-4 Software package for multivariate statistics, official R package since 2002
DICROPROT Analysis of circular dichroism spectra
AnTheProt Graphical user interface for protein sequence analysis and molecular graphic display (Windows systems)

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Filed Under: Genomics