September 1, 2017
We are happy to announce a major update of our JSpeciesWS system, the free online service for genome-based taxonomic assignment and identification of prokaryotes. The improvement focuses on two main aspects, (1) redesign of the cart/analysis interface for better navigation (without removal of any major function) and (2) change to a new genome data resource for improved quality and sustainability, plus new data integration features (such as type strain and risk group information).
Source of the JSpeciesWS internal reference database GenomesDB is now Ensembl Bacteria as provided by the European Bioinformatics Institute (EMBL-EBI), currently offering about 43k taxonomically annotated public genome sequences. There are multiple advantages linked to this resource such as a clear and stable release cycle, standardised data formats, and long-term sustainability of the EMBL-EBI.
GenomesDB is enriching the original Ensembl data set with additional quality control and further contextual data integration from other resources. It will be regularly updated and we are working on new data integration and curation features for even more usability.
The system is freely available for research purposes (both academic and non-academic users) at jspecies.ribohost.com/jspeciesws (current system version is 3.0.x with GenomesDB release version 35).
For further introduction, please switch to our internal JSpeciesWS information page (direct link).
April 13, 2017
The AQUAVALENS consortium, which Ribocon is part of, seeks for improved molecular methods for the detection of pathogens in drinking water and water used in food preparation. While next generation sequencing (NGS) technology (such as provided by Illumina) has become a standard tool for the description of complex microbial communities it has not yet been used for the "diagnostic" characterisation of selected target groups at species level resolution.
Supporting AQUAVALENS partner Helmholtz Centre for Infection Research, Ribocon is now involved in one of the first descriptions of an NGS-based approach for the monitoring of selected target organisms (here Legionella microbiomes in freshwater).
Detailed information you find under the DOI: 10.1186/s12866-017-0987-5 (open access article in BMC Microbiology).
January 27, 2017
As outlined in our webpage section on Networking, we are continuously collaborating with selected resources of microbial systematics to foster the creation of synergies between the academic fundament and the technical potential of applied bioinformatics. One of the outstanding resources of the last two decades is represented by the List of Prokaryotic names with Standing in Nomenclature (LPSN) which provides an integrated, up-to-date, electronic overview on all validly published prokaryotic species, including their classification.
Since early 2016, Ribocon is actively supporting LPSN by means of optimizing the database infrastructure and applying extra quality control procedures to improve system sustainability over time. The main outcome of the hitherto collaboration was the release of a thorough update (first after three years) of the LPSN classification of domains and phyla page based on a now standardised and mainly automated process in October 2016. This advancement will also allow for more regular updates of the LPSN classification pages in the future.
Furthermore, we are proud of having contributed to the Bergey's Manual of Systematics of Archaea and Bacteria, the central authority of prokaryotic systematics. In September 2016, the chapter on the marine and extreme halophile Archaea genus Halorhabdus was published under the support of Ribocon (phylogeny of the taxon).
Follow the links to the Bergey's Manual of Systematics of Archaea and Bacteria and the Bergey's Manual Trust for additional information.
September 8, 2016
We are happy to introduce the new Ribocon web appearance. It features a new and fully responsive layout for access by any device, as well as a sharpened company profile and detailed information on our portfolio.At the same time we started a Ribocon Twitter channel and updated our LinkedIn company profile, allowing you to easily receive our latest news. Thank you for following us!
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