Archive for décembre, 2009

Databases

Posted on décembre 26, 2009 by Commentaires fermés

ReNaBi’s platforms are providing many databases that represent key resources for the community.

These databases cover a wide range of topics:

Here is a listing of these databases.

Virus databases

GiantVirus Database on giant viruses
euHCVdb European Hepatitis C Virus database

Microbial sequence databases

PlasmoDraft Database of Plasmodium falciparum gene function predictions based on postgenomic data
GenoList Integrated database for microbial genomes, with specialisation in population genomics of pathogens
CandidaDB Multi-genome database for Candida species and related Saccharomycotina
Molligen Database for comparative genomics of mycoplasma genomes; It contains about 20 bacterial (mycoplasma) (re)-annotated genomes
NORINE Unique database of nonribosomal peptides
CRISPRdb Database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
GPMS Microbes Tandem Repeats Database Database of tandem repeats in microbes; On-line resources for bacterial micro-evolution studies
PkGDB Microbial genomes database for annotation and comparative analysis; >700 bacterial (re)-annotated genomes
ISFinder Insertion sequence database and service on IS expertise
COBALT Provides easy access to the results of multiple localization tools and support for predicting protein subcellular localizations for 784 whole bacterial and archaeal proteomes
MICADO Relational database dedicated to microbial genomes and functional analysis of B. subtilis
MOSAIC Relational database and web interface developed to compare closely related bacterial genomes
SPID Subtilis Protein interaction Database
Funybase Database dedicated to the analysis of fungal proteins extracted from complete public fungal genomes, and their classification in clusters of orthologs

Plant & animal sequence databases

OryGenesDB Database interoperability for functional genomics of rice
GreenPhylDB Database for structural, functional and comparative annotation dedicated to plant genomes and their bio-aggressors
PROTICdb Web-based application to store, track, query, and compare plant proteome data
Sigenae Sigenae contig browser: Aquaculture and farm animal species EST contigs access through Ensembl and BioMart
AphidBase An aphid genomics database and query tools
DGD Provides a list of groups of co-located and duplicated genes
ASSEMBLE Tools Tools and Databases dedicated to access of marine resources (ABiMS resource)
MICROBASE Microbotryum violaceum EST relational database
GnpIS Genetic & Genomic Information System with modular and interoperable databases and query interfaces allowing to query each database independently or in combination; it contains genetic (polymorphism, genotypes, phenotypes) and genomic data (sequences, mapping, expression…) from plant and fungi genomes (wheat, grapevine, maize, trees, fungi…)

Human databases

ITTACA A database of transcriptome arrays and clinical data of tumours
ACTuDb A database of array-CGH data of tumours
GENATLAS Contains relevant information with respect to gene mapping and genetic diseases; the information is collected from the literature
MIRIFIX Both an integrated database with its own developments and a dynamic portal to the most up-to-date and relevant webtools for non-coding RNA (miRNA); MIRIFIX(TM) enables questioning of microRNAs at each levels of action through a single interface
Atlas of Genetics and Cytogenetics in Oncology and Haematology The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases.

Immunogenetics databases

IMGT/LIGM-DB The IMGT® database for the nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR) from human and other species of vertebrates, with translation of fully annotated sequences, created in 1989, on the Web since July 1995; 150,000 sequences from 254 species (human and other vertebrates)
IMGT/PRIMER-DB The IMGT® oligonucleotide database: Primers for combinatorial library constructions, single chain Fragment variable (scFv), phage display or microarray technlologies; 1,864 entries from 11 species (human and other vertebrates)
IMGT/GENE-DB The IMGT® gene database: Official repository of all the immunoglobulin (IG) and T cell receptor (TR) genes and alleles, approved by the WHO/International Union of Immunological Societies Nomenclature Subcommittee
IMGT/3Dstructure-DB The IMGT® 3D structure database: 3D structures of Immunoglobulins (IG), T cell receptors (TR), MHC, IgSF, MhcSF and related proteins of the immune system (RPI), created in November 2001; Repository of the amino acid sequences of the monoclonal antibodies and fusion proteins for immune applications (FPIA) of the WHO/International Nonproprietary Name (INN) programme
IMGT/mAb-DB The IMGT® database of therapeutic monoclonal antibodies and fusion proteins for immune applications (FPIA), created in 2009
IMGT/CLL-DB IMGT/CLL-DB, the IMGT® database of IG sequences from patients with chronic lymphocytic leukemia, created in November 2007

Protein & motif databases

MIPDB Database for intrinsic membrane proteins
PROSE Relational version of UniProt
HOVERGEN, HOGENOM & HOMOLENS Set of databases devoted to protein gene families
AT_Chloro Chloroplast proteome from Arabidopsis thaliana database
PRODOM Database of protein domains, part of the InterPro network

Enzyme & pathway databases

RBpathway Database of RB/E2F network
FUNGIpath Database and tool dedicated to metabolism pathway exploration in fungi; it currently contains 20 genomes data (Release 1.0, February 2009)
ORENZA Database of ORphan ENZyme Activities
Peroxibase Centralize most of the peroxidase superfamilies encoding sequences to follow the evolution of peroxidase among living organisms and to compile the information concerning putative functions and transcription regulation
MetExplore Database to link metabolomic experiments and genome-scale metabolic networks
PAREO Relational version of KEGG
UniPathway Curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase

High-throughput data repositories

GERMONLINE High-throughput expression data relevant for germline development across species (it includes data on the mitotic cell cycle in normal and malignant cells)
SIDR Standard-compliant metadata database with raw and/or processed associated data in Sytems biology

Other databases

GlycoBase Database of real NMR spectra concerning glycans from animal kingdom
ACNUC Sequence database management system for any collection in GenBank, EMBL or UniProt format

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Filed Under: Databases

Proteomics

Posted on décembre 25, 2009 by Commentaires fermés

The ProteHome website, hosted by PRABI,  is a portal dedicated to resources for experimental proteomics by making these available to the scientific community. The aim of ProteHome is to contribute directly to the set up of services and resources for experimentalist and computer scientist involved in proteomics analysis and data handling.

MyProms An environment for mass spectrometry data management and analysis
PASE A web-based platform for peptide / protein microarray experiments.
ASCQ_ME Engine for peptide mass fingerprinting directly from mass spectrum

Filed Under: Proteomics

ALPHY 2010

Posted on décembre 17, 2009 by Commentaires fermés

La réunion ALPHY 2010 aura lieu les 2 et 3 février 2010 à Marseille.

Cette réunion rassemble depuis plus de 15 ans la communauté francophone
autour des mots clés Phylogénie, Alignement, Génomique comparative et
Bioinformatique.
La réunion comprendra deux présentations longues par Eduardo Rocha et David Moreira
(orateurs invités), et une vingtaine de présentations de 25 minutes sur soumission. Comme
tous les ans, la priorité sera donnée
aux jeunes chercheurs, et aux chercheurs ne s’étant pas exprimés les
années précédentes.

Pour soumettre un exposé, merci d’envoyer un titre et résumé à
alphy2010@ifr88.cnrs-mrs.fr avant le *** 3 janvier 2010 ***.

La réunion se tiendra dans la salle de conférence Pierre Desnuelle du campus CNRS Joseph
Aiguier.
Délégation Régionale CNRS 12
31 chemin Joseph Aiguier
13009 Marseille

Un plan d’accès et les informations pratiques sont disponibles
sur le site web de la réunion: http://lcb.cnrs-mrs.fr/spip.php?article347

L’inscription est gratuite mais obligatoire par mail (alphy2010@ifr88.cnrs-mrs.fr)
ou sur le site web (http://lcb.cnrs-mrs.fr/spip.php?article347).

Filed Under: News

Algorithmique, combinatoire du texte et applications en bio-informatique.

Posted on décembre 8, 2009 by Commentaires fermés

Algorithmes et combinatoire du texte et applications en bioinformatique

Les 25 et 26 janvier 2010 se tiendront à Montpellier les journées Algorithmique, combinatoire du texte et applications en bio-informatique.
Elles sont organisées conjointement par l’axe « analyse de séquences » du GDR Bio-Informatique Moléculaire (3003) et le groupe de travail COMATEGE du GDR Informatique Mathématique.
Les thèmes abordés vont de la combinatoire et de l’algorithmique du texte et leurs applications à l’analyse bio-informatique des séquences biologiques. Cela inclut les sujets suivants, sans y être limité :

  • algorithmes du texte
  • structures d’indexation
  • combinatoire des mots
  • recherche, découverte et analyse de motifs
  • statistique des mots
  • analyse de séquences
  • cartographie et annotation des génomes
  • haplotypes et polymorphismes
  • approches ab initio et approches comparatives
  • méthodes de génomique comparative
  • outils d’analyse des répétitions génomiques
  • analyse des données de séquençage haut-débit (SHD, NGS)

Les exposés seront organisés par session avec des sensibilités plus informatique, mathématique, ou bio-informatique.
L’inscription est gratuite mais obligatoire. Vous pouvez vous inscrire ou proposer un exposé dès maintenant. Les modalités sont disponibles à http://www.lirmm.fr/mab/gtseq

Filed Under: News

RPBS

Posted on décembre 8, 2009 by Commentaires fermés

logo_RPBS

RPBS was initiated in the late 2003. His objectives are :

  • to provide a means of collaborative research in the field of structural bioinformatics at the level of Paris and beyond.
  • to provide some compendium of the services related to protein structure.

It is currently a joint effort of the following research groups from Paris.

  • MTi – Molécules thérapeutiques in silico – INSERM U973 – Université Paris 7
  • DSIMB – Dynamique des Structures et Interactions des Macromolécules Biologiques – INSERM U665 – Université Paris 7
  • ABI – Atelier de BioInformatique – Université Paris 6
  • IMPMC – Equipe Prédiction des Structures – CNRS UMR 7590 – Université Paris 6 et 7
  • IBBMC-MIP – Groupe Théorique de l’Equipe de Modélisation et Ingénierie des Protéines – CNRS UMR 8619 – Université Paris-sud 11
  • CNAM-STIC – Chaire de Bioinformatique, Conservatoire National des Arts et Metiers, Paris
  • MAP5 – Mathématiques Appliquées à Paris 5 – CNRS UMR 8145 – University Paris Descartes

Project coordination: P. Tufféry



Site web : RPBS

Filed Under: Sites

PRABI

Posted on décembre 8, 2009 by Commentaires fermés

logoprabi_small209

The PRABI is the Rhône-Alpes Bioinformatics Center, a RIO platform of the Rhône-Alpes Genopole. It gathers many research teams that develop new biological modeling using mathematics and computer sciences. The PRABI provides to the national and international community the computer tools that result from these researches. Moreover some « classical » tools of bioinformatics are also available. However it is not the aim of PRABI to compete with big international centers (as EBI, NCBI, …) on which a much larger collection of tools can be found.

The PRABI expects to be an exchange tool between biologists and bioinformatic researchers. This site aims at presenting the databases and computational tools available through the PRABI for biology and health research.

Rhone-Alpes BioInformatics Center

The Rhone-Alpes BioInformatics Center is a platform gathering 11 research teams spread on 4 different sites. the PRABI has research, service and training activities in a large number of bioinformatics and biostatistics fields.



Web site : PRABI

Filed Under: Platforms

BIPS Strasbourg

Posted on décembre 8, 2009 by Commentaires fermés

The IGBMC Bioinformatics Platform is a high-throughput platform for comparative and structural genomics.
Its goal is to:
collect, maintain and deliver to the scientific community a wide range of bioinformatics resources addressing biological issues from studies of normal or pathological cells and genes to drug discovery.
develop innovative solutions and participate actively in local, regional, national and international scientific programs.
diffuse the software and databases developped by the Laboratoire de Bio-informatique et Génomique Intégratives, including analysis tools for high throughput functional or structural genomics and integrative biological studies.
share and diffuse its knowledge and expertise by organising and participating in conferences and educational courses.
The platform is accessible for external laboratories at the local, regional, national and international levels.
The Strasbourg Bioinformatics Platform was identified in 2003 as Plate-forme Nationale RIO and Génopôle Grand-Est – « from gene to drug ».
In order to meet at best the requirements of its users, partners and collaborators, the platform initiated in january 2005 a Quality Managenent System inspired from the ISO9001:2000 norm.

logo-IGBMC

The IGBMC Bioinformatics Platform is a high-throughput platform for comparative and structural genomics.

Its goal is to:

  • collect, maintain and deliver to the scientific community a wide range of bioinformatics resources addressing biological issues from studies of normal or pathological cells and genes to drug discovery.
  • develop innovative solutions and participate actively in local, regional, national and international scientific programs.
  • diffuse the software and databases developped by the Laboratoire de Bio-informatique et Génomique Intégratives, including analysis tools for high throughput functional or structural genomics and integrative biological studies.
  • share and diffuse its knowledge and expertise by organising and participating in conferences and educational courses.

The platform is accessible for external laboratories at the local, regional, national and international levels.

In order to meet at best the requirements of its users, partners and collaborators, the platform initiated in january 2005 a Quality Managenent System inspired from the ISO9001:2000 norm.


Site web : BIPS

Filed Under: Sites

RNAspace

Posted on décembre 6, 2009 by Commentaires fermés

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. This service is provided by GenoToul.
The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an in silico environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.

RNAspace home page

RNAspace home page


Web site : RNAspace

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Filed Under: Platforms

GenOuest

Posted on décembre 6, 2009 by Commentaires fermés

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

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

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