

MicroScope
- Information
- Infrastructure
- Data
- Tools
- Expertise
- Trainings
- Collaborations
- Ouverture
- Imports
- Gerer mes utilisateurs
Adress
Structure(s)
Unit:
Website
MicroScopeScientific leader(s)
Technical leader(s)
Certificat(s)
- France-Génomique
- ISO 9001
- Label IBiSA
- NF X50-900
![]() Annual visits: 55 000 an
Unique visits: 11 000 an
Quotes: 910
Downloads: Not documented
MicroScopeDescriptionLocated at Genoscope (CEA sequencing center for environmental genomics), the LABGeM bioinformatics team has developed MicroScope, a web-based platform for prokaryotic genome analysis and expert functional annotation. MicroScope combines tools and graphical interfaces to analyze genomes and to perform manual curation of gene function in a comparative and metabolic context. This platform provides data from completed and ongoing genome projects together with post-genomic experiments (i.e. transcriptomics, re-sequencing of evolved strains) allowing users to improve the understanding of gene functions. Expert annotations are continuously gathered in the MicroScope database contributing to the improvement of the quality of microbial genome annotations, and thus to the predicted metabolic networks. MicroScope can be used as a community resource for comparative analysis and annotation of publicly available genomes but also as a private resource with restricted access rights on genomic data. In addition, we regularly hold professional trainings sessions on the use of MicroScope platform. Access conditions
Service features:
More details here. |
Domains of activity
- Biomedical
- Agri-food
- Environment
- Biotechnology
Description of expertise domains
- Tools and databases for bacterial genome annotation and comparative genomics
- Metabolic network reconstruction
- Curation of metabolic data
- Discovery of new enzymatic activities
- Quantitative transcriptomics via RNA-seq
- Variant analysis
- Pangenomics and (meta)genomics analyses
Keywords:
- NGS data analysis
- Methodology
- Read mapping
- Genomics (DNA-seq)
- Genome analysis
- Transcriptomics (RNA-seq)
- Differential gene expression analysis
- Transcripts and transcript variants analysis
- Variant calling
- Whole genomes
- Metagenomics, metatranscriptomics
- Sequence algorithmics
- (multiple) Sequence Alignment
- Sequence annotation
- Sequence motif discovery
- Homology/Orthology prediction
- Machine learning
- Knowledge extraction
- Integration of heterogeneous data
- Knowledge representation
- System biology
- Metabolic network modelling
- System modelling
- Data curation
- Information and communication technology developments
- Tools
- Tool integration
- Interoperability
- Interfaces, web portals
- Workflows developments
- Data integration
- Data management and transfer
- Databases and information systems
- Comparative genomics
- Genome comparison
- Comparison of functional and regulatory pathways
Formation professionnelle
![]() Trainees: 30 trainees / year
Training time: 10 day(s) / year
No upcoming session scheduled
Formations à la plate-forme MicroscopeDescriptionThe LABGeM team at Genoscope regularly organizes training courses dedicated to the analysis of bacterial genomes via the use of the MicroScope platform at the University of Évry.
Each session is made up of half theory and half practical work. During the training, participants have the opportunity to work on their own data during practical work.
Access conditionsFor more information and registration : https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/. |
Formation universitaire
![]() Trainees: 50 trainees / year
Training time: Not documented
No upcoming session scheduled
Formation universitaireDescriptionLABGeM's researchers are involved in different training programs in collaboration with :
Access conditionsNot documented |
Internal publications
Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fevre, F., Longin, C., Mornico, D., Roche, D., Rouy, Z., Salvignol, G., Scarpelli, C., Thil Smith, A. A., Weiman, M. & Médigue, C. (2013).
"MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data." Nucleic Acids Res 41(Database issue): D636-647.
Belda, E., Sekowska, A., Le Fevre, F., Morgat, A., Mornico, D., Ouzounis, C., Vallenet, D., Médigue, C. & Danchin, A. (2013). "An updated metabolic view of the Bacillus subtilis 168 genome." Microbiology 159(Pt 4): 757-770.
External publications
Publications with the hosting laboratory
Users distribution
Explanation about this distribution:
From <400 user accounts in 2006, MicroScope counts >4200 personal accounts at present time. The number of registered users has doubled since 2013, and the platform has even widened its international popularity with 64% of accounts outside France.
Many international projects are conducted through the platform involving users from distant geographic areas. Although authentication is not required to navigate in MicroScope, it allows users to annotate genes and save data on their personal session.
On average per month, we count 360 active accounts (i.e. the user logged in at least once in the month).
Platform's own projects
- Tools for bacterial genome annotation and comparative genomics
- Metabolic network reconstruction
- Curation of metabolic data
- Discovery of new enzymatic activities
- Quantitative transcriptomics via RNA-seq
- Variant analysis
- Pangenomics and (meta)genomics analyses
Collaborations
National projets
REPLICOLSCOPE (ANR GENOM 2011-2015) ; VIBRIOGEN: (ANR Blanc 2011-2015) ; SHAPE (ANR BioAdapt 2012-2016) ; BugInACell (ANR Blanc 013-2017) ; BLUE ENZYMES (ANR “Sécurité alimentaire et défi démographique” 2014-2018) ; MOPAD (projet BPI 2014-2017)
France Génomique (FG) - Développements méthodologiques pour le workpackage 2.7.2 de FG: annotation et analyse de métagénomes (2012-2016)
Institut Français de Bioinformatique (IFB) – Développements méthodologiques pour la thématique “Microbial bioinformatics” de l’IFB (2013-2016)
SYNBIOWATCH (NRBC programme transversal du CEA 2011-2015)
International and European projects
MetaCat (EU ERA NET 2015) ; ELIXIR (WS « Data and Resources »)
Projects with industry
Contrat de service avec DANONE RESEARCH (depuis 2010)
MOPAD (projet BPI en partenariat avec LIMAGRAIN & BIOVITIS Sept. 2014-2017)