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MicroScope

MicroScope

Adress
2, rue Gaston Crémieux, CP 5706 91057 Evry
Structure(s)
CEA, CNRS
Unit:
LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay
[field_pole_regional_de_rattachem]
Website
MicroScope
Scientific leader(s)
Scientific leader
Not documented
Technical leader(s)
Technical leader
Not documented
Certificat(s)
  • France-Génomique
  • ISO 9001
  • Label IBiSA
  • NF X50-900
Check the website
Annual visits:
55 000 an
Unique visits:
11 000 an
Quotes:
910
Downloads:
Not documented

MicroScope

Description

Located 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
  • Free for academics.
  • Sales quote available on demand for non-academics 

Service features:

  • Microbial genome annotation (complete, WGS or metagenome-assembled genomes)
  • Comparative genomics and pangenomics
  • Function and biological process predictions
  • Metabolic network reconstruction 
  • Analysis of transcriptomics data
  • Variant calling of evolved strains
  • Technical support
  • Trainings on prokaryotic genome annotation  and on the curation of metabolic networks 

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

Check the website
Trainees:
30 trainees / year
Training time:
10 day(s) / year
No upcoming session scheduled

Formations à la plate-forme Microscope

Description

The 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.
 
The course "Annotation and analysis of prokaryotic genomes using the MicroScope platform" lasting 4.5 days is aimed at:

  • acquiring theoretical and practical knowledge of genome annotation tools (structural and functional annotation, metabolic networks annotation)
  • knowing how to interpret the results of functional annotation tools
  • knowing how to carry out various comparative analyzes: analyzes of conserved syntenia, pan-genomes, phylogenetic and metabolic profiles
  • learning to interpret the results of metabolic network prediction tools and search for candidate genes for enzymatic activities
  • applying those tools to the analysis of genomes of interest to the participants 

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.
 
This training is aimed at doctoral students, engineers, researchers, experienced biological or medical laboratory technicians. It concerns both people who already have an annotation project on the MicroScope platform and wishing to deepen its use, as well as those wishing to learn microbial genomics.
 
 
In addition, if you are a user of the MicroScope platform and you have already followed the training "Annotation and analysis of prokaryotic genomes using the MicroScope platform" a few years ago we have implemented a new training , the "MicroScope Platform - Advanced Course" training in order to update your knowledge on the latest evolutions of the platform and to deepen some of its major functionalities.
 
This training, lasting 2 days, will consolidate your use of the platform but also go further:

  • Presentation of the evolutions of the MicroScope platform
  • Presentation of the new flagship features of the MicroScope platform
  • Presentation of tools for RNA-seq analyzes
  • Deepening of the functionalities allowing the exploration of the bacterial metabolism
Access conditions

For more information and registration : https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/.

Formation universitaire

Check the website
Trainees:
50 trainees / year
Training time:
Not documented
No upcoming session scheduled

Formation universitaire

Description

LABGeM's researchers are involved in different training programs in collaboration with :

  • the University of Paris Saclay: master GENIOMHE, master MSSB, master NRBCe
  • the University Denis Diderot: master M2BI
  • the University Paris Descartes: master IMVI
  • the Institut Pasteur: Training ‘Analyse des génomes’
Access conditions
Not 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.


Sorokina M., Stam M., Médigue C., Lespinet O. and Vallenet D. (2014). "Profiling the orphan enzymes." Biol Direct 9: 10.

Calteau A, Fewer DP, Latifi A, Coursin T, Laurent T, Jokela J, Kerfeld CA, Sivonen K, Piel J, Gugger M. (2014). "Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria." BMC Genomics 15: 977.
External publications
Goudenege, D., Labreuche, Y., Krin, E., Ansquer, D., Mangenot, S., Calteau, A., Médigue, C., Mazel, D., Polz, M. F. & Le Roux, F. (2013). "Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits." ISME J 7(10): 1985-1996.

Guan, S. H., Gris, C., Cruveiller, S., Pouzet, C., Tasse, L., Leru, A., Maillard, A., Médigue, C., Batut, J., Masson-Boivin, C. & Capela, D. (2013). "Experimental evolution of nodule intracellular infection in legume symbionts." ISME J 7(7): 1367-1377.

Humbert, J. F., Barbe, V., Latifi, A., Gugger, M., Calteau, A., Coursin, T., Lajus, A., Castelli, V., Oztas, S., Samson, G., Longin, C., Médigue, C. & de Marsac, N. T. (2013). "A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa." PLoS One 8(8): e70747.

Kristiansen, R., Nguyen, H. T., Saunders, A. M., Nielsen, J. L., Wimmer, R., Le, V. Q., McIlroy, S. J., Petrovski, S., Seviour, R. J., Calteau, A., Nielsen, K. L. & Nielsen, P. H. (2013). "A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal." ISME J 7(3): 543-554.

Leikoski, N., Liu, L., Jokela, J., Wahlsten, M., Gugger, M., Calteau, A., Permi, P., Kerfeld, C. A., Sivonen, K. & Fewer, D. P. (2013). "Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides." Chem Biol 20(8): 1033-1043.

Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN. (2013). "Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26." Genome Biol Evol 5(5): 934-953.

Le Gac M, Cooper TF, Cruveiller S, Médigue C, Schneider D. (2013). "Evolutionary history and genetic parallelism affect correlated responses to evolution." Mol Ecol 22(12): 3292-3303.

Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R., Herdman, M., Sivonen, K., Coursin, T., Laurent, T., Goodwin, L., Nolan, M., Davenport, K. W., Han, C. S., Rubin, E. M., Eisen, J. A., Woyke, T., Gugger, M. & Kerfeld, C. A. (2013). "Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing." Proc Natl Acad Sci U S A 110(3): 1053-1058.

Supply, P., Marceau, M., Mangenot, S., Roche, D., Rouanet, C., Khanna, V., Majlessi, L., Criscuolo, A., Tap, J., Pawlik, A., Fiette, L., Orgeur, M., Fabre, M., Parmentier, C., Frigui, W., Simeone, R., Boritsch, E. C., Debrie, A. S., Willery, E., Walker, D., Quail, M. A., Ma, L., Bouchier, C., Salvignol, G., Sayes, F., Cascioferro, A., Seemann, T., Barbe, V., Locht, C., Gutierrez, M. C., Leclerc, C., Bentley, S. D., Stinear, T. P., Brisse, S., Médigue, C., Parkhill, J., Cruveiller, S. & Brosch, R. (2013). "Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis." Nat Genet 45(2): 172-179.

Sugawara, M., Epstein, B., Badgley, B., Unno, T., Xu, L., Reese, J., Gyaneshwar, P., Denny, R., Mudge, J., Bharti, A. K., Farmer, A. D., May, G. D., Woodward, J. E., Médigue, C., Vallenet, D., Lajus, A., Rouy, Z., Martinez-Vaz, B., Tiffin, P., Young, N. D. & Sadowsky, M. J. (2013). "Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies." Genome Biol 14(2): R17.

Wielgoss, S., Barrick, J. E., Tenaillon, O., Wiser, M. J., Dittmar, W. J., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E. & Schneider, D. (2013). "Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load." Proc Natl Acad Sci U S A 110(1): 222-227.

Zoropogui, A., Pujic, P., Normand, P., Barbe, V., Belli, P., Graindorge, A., Roche, D., Vallenet, D., Mangenot, S., Boiron, P., Rodriguez-Nava, V., Ribun, S., Richard, Y., Cournoyer, B. & Blaha, D. (2013). "The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle." BMC Genomics 14: 286.

Ji, B., Zhang, S. D., Arnoux, P., Rouy, Z., Alberto, F., Philippe, N., Murat, D., Zhang, W. J., Rioux, J. B., Ginet, N., Sabaty, M., Mangenot, S., Pradel, N., Tian, J., Yang, J., Zhang, L., Zhang, W., Pan, H., Henrissat, B., Coutinho, P. M., Li, Y., Xiao, T., Médigue, C., Barbe, V., Pignol, D., Talla, E. & Wu, L. F. (2014). "Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain." Environ Microbiol 16(2): 525-544.

Plucain J, Hindré T, Le Gac M, Tenaillon O, Cruveiller S, Médigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE, Schneider D. (2014). "Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli." Science 343(6177): 1366-1369.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D. (2014). "Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli." MBio 5(5): e01377-01314.

Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EP, Masson-Boivin C. (2014). "Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer." PLoS Biol 12(9): e1001942.

Billard-Pomares T, Fouteau S, Jacquet ME, Roche D, Barbe V, Castellanos M, Bouet JY, Cruveiller S, Médigue C, Blanco J, Clermont O, Denamur E, Branger C. (2014). "Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum beta-lactamase from an Escherichia coli strain." Antimicrob Agents Chemother 58(11): 6550-6557.

de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L. (2014). "RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti." Genome Biol Evol 6(4): 932-948.

Ramos PI, Picão RC, Almeida LG, Lima NC, Girardello R, Vivan AC, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Médigue C, Vasconcelos AT, Gales AC, Nicolás MF. (2014). "Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms." BMC Genomics 15: 54.

Ogier JC, Pagès S, Bisch G, Chiapello H, Médigue C, Rouy Z, Teyssier C, Vincent S, Tailliez P, Givaudan A, Gaudriault S. (2014). "Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii." Genome Biol Evol 6(6): 1495-1513.

Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J. 2014 Dec 9. doi: 10.1038/ismej.2014.233. [Epub ahead of print].

Goudenège D, Travers M, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A, Le Roux F. (2014). "A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters." Environ Microbiol.

Gomez-Valero L, Rusniok C, Rolando M, Neou M, Dervins-Ravault D, Demirtas J, Rouy Z, Moore RJ, Chen H, Petty NK, Jarraud S, Etienne J, Steinert M, Heuner K, Gribaldo S, Médigue C, Glöckner G, Hartland EL, Buchrieser C. (2014). "Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease." Genome Biol 15(11): 505.

Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P. (2014). "genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?" PLoS One 9(9): e108522.

Moulin, L., Mornico, D., Melkonian, R. & Klonowska, A. (2013). "Draft Genome Sequence of Rhizobium mesoamericanum STM3625, a Nitrogen-Fixing Symbiont of Mimosa pudica Isolated in French Guiana (South America)." Genome Announc 1(1).

Lanois, A., Ogier J. C., Gouzy, J., Laroui, C., Rouy, Z., Givaudan, A. & Gaudriault, S. (2013). "Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1." Genome Announc 1(3).

Kits, K. D., Kalyuzhnaya, M. G., Klotz, M. G., Jetten, M. S., Op den Camp, H. J., Vuilleumier, S., Bringel, F., Dispirito, A. A., Murrell, J. C., Bruce, D., Cheng, J. F., Copeland, A., Goodwin, L., Hauser, L., Lajus, A., Land, M. L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Zeytun, A. & Stein, L. Y. (2013). "Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8." Genome Announc 1(2): e0017013.

Ji, B., Gimenez, G., Barbe, V., Vacherie, B., Rouy, Z., Amrani, A., Fardeau, M. L., Bertin, P., Alazard, D., Leroy, S., Talla, E., Ollivier, B., Dolla, A. & Pradel, N. (2013). "Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.)." Genome Announc 1(1).

Amin, O., Fardeau, M. L., Valette, O., Hirschler-Rea, A., Barbe, V., Médigue, C., Vacherie, B., Ollivier, B., Bertin, P. N. & Dolla, A. (2013). "Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T)." Genome Announc 1(1).

Zhang SD, Barbe V, Garel M, Zhang WJ, Chen H, Santini CL, Murat D, Jing H, Zhao Y, Lajus A, Martini S, Pradel N, Tamburini C, Wu LF. (2014). "Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200." Genome Announc 2(2).
Publications with the hosting laboratory
Bastard K, Smith AA, Vergne-Vaxelaire C, Perret A, Zaparucha A, De Melo-Minardi R, Mariage A, Boutard M, Debard A, Lechaplais C, Pelle C, Pellouin V, Perchat N, Petit JL, Kreimeyer A, Médigue C, Weissenbach J, Artiguenave F, De Berardinis V, Vallenet D, Salanoubat M. (2014). "Revealing the hidden functional diversity of an enzyme family." Nat Chem Biol 10(1): 42-49.

Stuani L, Lechaplais C, Salminen AV, Ségurens B, Durot M, Castelli V, Pinet A, Labadie K, Cruveiller S, Weissenbach J, de Berardinis V, Salanoubat M, Perret A. (2014). "Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach." Metabolomics 10(6): 1223-1238.
Users distribution
International
60 %
National
25 %
Regional
10 %
Local
5%
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)

Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )
Not documented
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