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A key aim of the SIMBA project is to provide a better understanding of the microbiome structures and functions that are related to land and sea food chains. To support this, SIMBA partners have developed an open access database comprising microbiome data that can be used to identify microbiomes that will be useful in food production.
The SIMBA open-access database is an online platform for researchers to interact and explore large-scale metagenomic datasets within a user-friendly web interface. The developed platform consists of a scalable bioinformatics pipeline running within the powerful de.NBI cloud and an interactive web browser providing a high degree of flexibility for users to organize, summarize, and visualize their datasets of interest. The pipeline incorporates both, in-house developed tools and other state-of-the-art bioinformatics software that enables rapid screening of terabytes (TBs) of public datasets. The platform allows efficient extraction of relevant data and to deduce associations between public datasets and personal research interests.
You can access the web portal or submit your own data for analysis, please contact emgb-service@cebitec.uni-bielefeld.de to register an account.
Figure: An overview of the bioinformatics platform. A) A scalable bioinformatics pipeline for detecting microorganisms that are associated with plant growth promoting bacteria (PGPB). The pipeline consists of five different steps, starting with the collection of public datasets and PGPB genomes of interest. The results of the pipeline can be imported into the Elastic Metagenome Browser (EMGB). B) The web-based interactive metagenomics browser platform EMGB. The browser mainly displays five result categories: genome assemblies, MAGs compiled by metagenome binning, de-replicated MAGs, abundance profiles of the de-replicated MAGs, and predicted genes with their functional annotations.