We are pleased to announce the first release of MarFun, a database for marine fungi. The first version contains 21 manually curated genomes. MarRef and MarDB have been updated to version four, which contains 945 and 12972 entries respectively. MarDB contains now more MAGs (Metagenome Assembled Genomes) than WGSs (Whole Shotgun Sequenced) and SAGs (Single Amplified Genomes) together, with 7053, 4902 and 1017 entries, respectively. The quality of each genome is now provided using the CheckM output completeness (%), contamination (%) and QS (Quality Score = completeness - 5 x contamination).
MarRef and MarDB v3 is now available for browsing, blasting and downloading. MarRef and MarDB contains now 839 complete and 10869 non-complete genomes, respectively. We have improved the curation of many attributes by implemented Controlled Vocabulary (CV) e.g. for “Analysis project type” contain only the terms Whole genome sequencing (WGS), Metagenome assembled genome (MAG) and Single amplified genome (SAG). We have included a “MAR Download” page to ease the access to the contextual and sequence data in addition to microbial genomics and metagenomics resources generated from the MAR databases.
We are pleased to announce the release of MarRef and MarDB v2. We have added 174 and 4942 new genomes to MarRef and MarDB, respectively, bringing the total number of MAR genomes to approximately 9500. The redesigned database schema and web user interface support several new features including the implementation of predicted secondary metabolites obtained from antiSMASH and new attributes for a better description of MAGs (Metagenome Assembled Genomes). We have also improved the web application - the loading time of the databases has been substantially reduced.
The MAR databases are now available in JSON format. The MAR databases web application (MarRef, MarDB, MarCat) now uses databases in JSON format instead of XML, this made it load up to 2.5 times faster. The MAR databases can be downloaded here.
The MAR databases was published 2nd Nov 2017 in Nucleic Acid Research (NAR) as a paper for the NAR Database issue 2018. In the paper “The MAR databases: development and implementation of databases specific for marine metagenomics” we describe how we build the databases and the content. The open access paper can be downloaded from NAR.
We have released an updated version of the MAR databases. MarRef contains now 612 complete genomes, MarDB 3726 incomplete genomes, and MarCat contains 1227 metagenomics samples.
ELIXIR published today the initial lists of ELIXIR Core Data Resources and Deposition Databases. The lists can be here
We have now included a HELP page to help our end-users to use the services provided by Marine Metagenomics Portal (MMP). In addition, we also included a FEEDBACK form. We hope the MMP users will take advantage of using the feedback, helping the MMP team to build a better working environment and improve our services.
We have released the Beta version of the MMP (Marine metagenomics Portal).
Our paper in the Elixir F10000 channel summarizes the results from the ELIXIR pilot action “Marine metagenomics – towards user centric services”.
META-pipe is an important demonstrator for the ELIXIR compute platform services as demonstrated in the webinar.
The design, implementation and evaluation of META-pipe 1.0 is described in this paper.
A practical workshop in marine metagenomics will be held during 7-11 May 2018, in Oeiras, Portugal hosted by the Portuguese ELIXIR Node in cooperation with ELIXIR Norway.
The Marine Metagenomics Use Case will be presented at the 12th CeBiTec Symposium Big Data in Medicine and Biotechnology, the Center for Interdisciplinary Research (ZiF), Bielefeld University, March 19 - 21, 2018
We are co-organizing the First Marine Microbiome workshop Metagenomics and Bioinformatics for Biodiversity in Nador, Morocco, 5-9 Feb. 2018.
We are invited to give a talk about marine metagenomics use case at the ELIXIR Innovation and SME Forum: Data-driven innovation in food, nutrition and the microbiome, taking place at the KVS - Brussels City Theatre, Brussels, October 9-10, 2017
See also the article on the Metagenomics course written by Eija Korpelainen (ELIXIR Finland) and Premysl Velek (ELIXIR Hub)
We will give talks, present posters, and a co-host a workshop at the ELIXIR all-hands meeting in Rome 21-23 March 2017.
The ELIXIR Norway node at UiT The Arctic University of Norway is arranging a 5 days hands-on workshop in marine metagenomics 26-30 nov. 2018 in collaboration with the ELIXIR Slovania EeLP team. The workshop is a part of the ELIXIR Marine Metagenomics Community outreach activities.