MicroScope platform

The MicroScope platform is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. The resource provides data from completed and ongoing genome projects together with post-genomic experiments (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections) allowing users to improve the understanding of gene functions.

The MicroScope platform is constantly evolving both in terms of data content and of new analysis tools some of them being developed in the context of our research projects.

Last news about MicroScope:

Removal of some obsolete GenBank assemblies

We have decided to remove assemblies which have been deleted from the GenBank database (see the list here). If you need these genomes for your analyses, you can request the integration of their current assembly version from this page ...
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MicroScope platform: v3.15.4 released

The version 3.15.4 of the platform is now deployed. The main novelty of this version is the introduction of Genome Carts. They are integrated in the Sequence/Organism selector so they can be selected quickly. This feature replaces the list of Favourite Organisms. Note that a cart can be selected as ...
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Electrical maintenance at Genoscope starting March 25th

Dear MicroScope users, MicroScope and LABGeM's website will be unavailable starting Friday March 25th around 5pm CEST. Everything should be back to normal for Monday March 28th 9am CEST. This is needed for an maintenance operation on the electrical network at Genoscope. We apologize for any inconvenience. The LABGeM Team ...
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MicroScope unavailability last week

Dear MicroScope users, As you may have noticed, MicroScope was unavailable or extremely slow between Thursday March 17th around 5pm CEST and Friday March 18th 10am CEST. This is due to an unexpected failure in our IT infrastructure. No data were lost and there should not be any significant delay ...
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About recent problems in MicroScope

Dear MicroScope users, You may have noticed an unusual number of problems in some tools recently (generally ending with a big red error message). This is due to an update in our SQL server that turned on a more strict mode hence some queries are now rejected (despite the results ...
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MicroScope platform: v3.15.3 released

The version v3.15.3 of the platform is now deployed: As mentioned in the last newsletter, you will be asked to update your personal information when upon login. Moreover you will be asked to update those information every year (see the Privacy Notice for more information). Note that the list of ...
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MicroScope maintenance December 17th – 20th

Dear MicroScope users, MicroScope will be off-line from Friday December 17th 12pm CEST to Monday December 20th around 2pm CEST. This long shut-down is needed to update several components of our IT infrastructure. Services opened the week before might take a little longer than usual to deliver but should stay ...
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Feedback on the 2020 satisfaction survey

In the spring of 2020, we conducted a satisfaction survey with over 1700 users of the MicroScope platform. With this survey we wanted to know more about the profile of our user community and their use of the platform for their current/future projects. You can find some statistics on the ...
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Genome selection by Metadata

In order to improve the selection of genomes, MicroScope 3.15.2 introduced the possibility to select genomes based on a subset of species-level metadata published in Joshua S. Madin et al., A synthesis of bacterial and archaeal phenotypic trait data. Sci Data 7, 170 (2020). This article unifies phenotypic and quantitative ...
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Faster integration for new genomes

In order to improve the processing time of the genome analysis, we chose to replace NCBI blast with Diamond version 2 to perform protein sequence alignments (i.e. synteny computations and alignments against UniProt). Internal tests showed that the results obtained were very similar to those of Blast using the "more-sensitive" ...
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