News

Ongoing improvement of our free JSpeciesWS online system for species assignment of genome-sequenced bacterial cultures

June 4, 2021

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JSpeciesWs is a free online system to measure the probability if two or more (draft) genomes belong to the same species by pairwise comparison. You can either compare own genome uploads, our integrated and curated public reference genomes (>50k), or a mixture of both.

In the last two years, we have constantly worked on the service and its backbone in order to guarantee sustainability of the genome reference data collection process, proper annotation of those data, and final deployment as our integrated database GenomesDB. Meanwhile, we are running a fully automated pipeline for tracing and addition of public type strain genomes of newly described bacterial species, including quality control before acceptance. Also implemented are regular automated checks and updates on taxonomic lineage, species (scientific) name, and corresponding NCBI Taxonomy ID of all GenomesDB entries.
Of course, we also invested significant time to further improve the general user experience of the service. For example, by providing a set of new data views per entry of GenomesDB, like contig/sequence statistics or a history on data updates.

A detailed summary of those improvements, the underlying data gathering and processing strategies, and on the current system status, you find in the news section of the JSpeciesWS webpage at jspecies.ribohost.com/jspeciesws/#news and within the supplemental documentation provided by the Help section of the system.

Have a look and accelerate your taxonomic genome analysis!

Since end of 2020, we are also official partner of the German ELIXIR node, organised as German Network for Bioinformatics Infrastructure – de.NBI, see their industry partner service list. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe with the goal to coordinate these so that they form a single infrastructure (see elixir-europe.org).

SILVA license model for commercial users changed with the new release 138 - now free of cost for any usage!

January 6, 2020

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With the latest SILVA release 138 (published Dec 16, 2019 - see also corresponding release information) the project has changed its license model as announced before: the datasets are now free of cost for any usage (academic/non-academic users) based on a Create Commons Attribution 4.0 (CC-BY 4.0) license.
The partnership of Ribocon and the SILVA project is of course not further affected by this modification (see information on our Networking activities).

In early 2019, SILVA has also received the status of an ELIXIR Core Data Resource, representing a set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe with the goal to coordinate these so that they form a single infrastructure.

[Update] Change of SILVA license model for commercial users in fall 2019 - free of cost for any usage

September 6, 2019

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With the upcoming full database release 138 which is now expected for October 2019 (see also latest news of the SILVA project), SILVA will resign the current dual licensing model and the data sets will become fully free also for commercial/non-academic users. By that change SILVA is following the idea of the Open Access initiative.

Major improvement of our free JSpeciesWS online service for the taxonomic comparison of genomes

September 1, 2017

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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 change to our internal JSpeciesWS information page (direct link).

Characterisation of Legionella
freshwater microbiomes down to
the species level by Illumina sequencing

April 13, 2017

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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).

Advances in Prokaryotic Systematics:
2016 Networking Synergies Revisited

January 27, 2017

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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.

New Ribocon Webpage launched

September 8, 2016

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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!