Marine Metagenomics Portal (MMP) publicly available

Marine Metagenomics Portal (MMP) publicly available

The marine databases; MarRef, MarDb, and MarCat was presented at the ELIXIR All-Hands meeting in Rome 21/3 2017, and are now public available. This project is an international deliverable in the ELIXIR-EXCELERATE project.

The marine resources, which have been implemented in the Marine Metagenomics Portal (MMP), are a collection of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy.

While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDb includes all sequenced marine prokaryotic genomes regardless of level of completeness. MarCat represent a gene (protein) catalogue of uncultivable (and cultivable) marine genes and proteins derived from metagenomics samples.

The first versions of MarRef and MarDb contain 484 and 2557 entries, respectively. Each record is build up of 104 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to organism and taxonomic information.

The contextual and sequence Mar databases and are available at https://mmp.sfb.uit.no/

For contact: mmp@uit.no


Supporting Innovation in Genomics and Health

ELIXIR Finland and ELIXIR Estonia held a successful two-day ELIXIR Innovation and SME Forum in Helsinki on 27-28 March 2017. 

The two-day event presented some of the bioinformatics resources in Genomics and Health available through ELIXIR and showcased several companies that are already using public data resources in their business.

Fifty attendees from companies, academic institutions and ELIXIR partners had a chance to hear introductions to ELIXIR activities in Europe, particularly in Finland and Estonia. Talks were given by two SMEs, Blueprint Genetics (Finland) and Protobios (Estonia), both active users of public data. Representatives of ELIXIR Nodes and companies also showcased their technologies, services and products in a series of flash talks.... Read more  

ELIXIR Beacons to facilitate sharing of genomics data in Europe

Scientists across the world can now discover and query data from genomics projects in six different countries in Europe. This has been a success of the ELIXIR collaboration with the Global Alliance for Genomics and Health (GA4GH) on the Beacon project which has been recently expanded and extended into 2017.

The Beacon Project is developing an open sharing platform that helps genomic data centres to make their data discoverable. Beacons allow researchers to query individual datasets to determine whether they contain a specific genetic variant of interest. For example, researchers can ask Beacons simple questions like, ‘Do your data resources have genomes with this allele at that position?’

The first stage of the project (2015-2016) resulted in lighting Beacons in five ELIXIR Nodes - Sweden, Finland, France, Switzerland and Belgium, and in the European Genome-phenome archive (EGA, a joint project of EMBL-EBI and the Center for Genomic Regulation in Barcelona, ELIXIR Spain). Another Beacon will soon be launched in ELIXIR Netherlands. Each ELIXIR Beacon makes one or more genomics datasets discoverable to the international research community.... Read more 

BioSchemas supports the discovery of public datasets

Guidelines recently published by Google for the discovery of science datasets help data providers to describe their datasets in a structured way using schema.org, enabling internet search engines to find and index rich metadata to better present scientific datasets The published guidelines draw on the metadata specifications for life-science datasets developed by BioSchemas. One of the early adopters of the specifications is the Omics Discovery Index (OmicsDI), which has been presented as a good practice example in recent Google Research Blog post. OmicsDI has been developed by EMBL-EBI and supported by BD2K, and is an active member of the BioSchemas community. It provides dataset discovery service across a heterogeneous, distributed group of -omics data from eight repositories across the world.

BioSchemas is an open community initiative driven by ELIXIR to improve interoperability of life-science data. Building on and extending the schema.org markup, Bioschemas develop a collection of specifications that provide guidelines for describing metadata about life science information. Besides life science datasets, BioSchemas is working on specifications for samples, phenotypes, data repositories or proteins sequences.

To support the work of Bioschemas, ELIXIR has recently launched the BioSchemas Implementation study. The main partners in the study are BBMRI, BD2K and FORCE11, however, it has support of over 40 stakeholders. The BioSchemas group for life science datasets includes representatives from PDBe, UniProt, Pfam, DataMed and DATS, Repositive, OmicsDI, Intermine and Google.... Read more 

Hungary becomes ELIXIR Member

Hungary has become the 21st Member to join ELIXIR, following the signature of the ELIXIR Consortium Agreement by Dr József Pálinkás, President of the National Research, Development and Innovation Office in Hungary. 

The ELIXIR Node in Hungary is currently under development. The ELIXIR Node will be led by the MTA Research Centre for Natural Sciences and coordinated by Professor Laszlo Patthy of the Institute of Enzymology within the Research Centre for Natural Sciences of the Hungarian Academy of Sciences. The focus of the Hungarian Node will be on novel tools, services and databases in the field of protein sequence and structure investigation, DNA sequence analysis and translational medicine. 

"Our membership in ELIXIR will help us sustain and safeguard our national investments in life sciences by linking our research community and resources to the ELIXIR infrastructure,” said Professor Laszlo Patthy. In turn, Europe and existing ELIXIR Nodes will benefit from Hungarian expertise and resources in systems and computational biology. 

Dr Niklas Blomberg, ELIXIR Director, said: "In just three years since its launch in December 2013, ELIXIR membership has skyrocketed from the six founding members to the current 21. I am delighted to welcome our Hungarian colleagues to ELIXIR and look forward to our collaboration. Hungarian Membership of ELIXIR will open up opportunities for new collaborations and will benefit both the Hungarian as well as European life-science and bioinformatics community.” 

ELIXIR publishes Position Paper on Interim Evaluation of Horizon 2020

In response to European Union's public consultation on the interim evaluation of Horizon 2020, ELIXIR has published its Position Paper on Horizon 2020, the European Union's funding programme for research and development. 

The Paper includes recommendations that could be adopted for the reminder of Horizon 2020, as well as several longer-term suggestions to consider for a successor programme... Read more  

Read more ELIXIR news  

 

Available position as group leader for "Tjenester for sensitive data" at USIT, Oslo.

News Item ELIXIR.NO newsletter no 2, 2015
The ELIXIR.NO project, coordinated by the University of Bergen and including the Universities in Oslo, Trondheim, Tromsø and Ås, is now into its third year. We have made great progress towards the aim to establish a Norwegian Node in Elixir, the pan-European infrastructure for bioinformatics.
News Item ELIXIR.NO newsletter no 3, 2016
 
News Item Presentation of the Norwegian Bioinformatics Platform in NBS nytt
 
CourseNewsItem Course News: RNA-seq and ChIP-seq Data Analysis Course
!! THE COURSE IS FULL !!   You may still  sign up on the waiting list via this link , should there be any openings. Do not sign up via any other links on this page, they will be ignored.   This three-day workshop is focused on analysis of RNA-seq and ChIP-seq data, using R/Bioconductor, Galaxy and other open-source tools.   It is aimed at graduate students and other researchers who are using, or planning to use, RNASeq or ChIP-Seq methods as part of their research. The course will focus on hands-on training in using modern data analysis methods. What will I learn? Brief lectures will illustrate the underlying principles and assumptions of relevant methods, and give insight into how biological knowledge can be generated from RNA-seq and ChIP-seq experiments. The emphasis is on practical exercises where participants analyze RNA-seq and ChIP-seq data under the guidance of the lecturers and teaching assistants.  What will it cover? The course covers experimental design, core concepts and statistical analysis of RNA-Seq and ChIP-Seq data ; participants will be encouraged to help one another and to apply what they have learned to their own research problems. The workshop will be hands-on, and you are required to bring your own laptop!   Topics include: alignment, quality control, visualisation, abundance estimation, differential expression, enrichment analysis and peak calling, and statistical analysis using R/Bioconductor.  
News Item Elixir.no Yearly Meeting Held in Oslo 13,14 January
Elixir.no Yearly Meeting Held in Oslo 13,14 January
News Item Norway becomes full member of ELIXIR!
 
News Item Available position as group leader for "Tjenester for sensitive data" at USIT, Oslo.
 
News Item Introduction to Microarray and Next Generation Sequencing Analysis using the R stastitical language
 
News Item Intensive course in High Throughput Sequencing technologies and bioinformatics analysis
The Oslo node of the ELIXIR Norway Bioinformatics Platform (Bioinformatics Core Facility), the Oslo node of the Norwegian Genomics Consortium (Genomics Core Facility) and the Norwegian Sequencing Centre are happy to invite you to an introductory hands-on course on analysis of next-generation sequencing data using bioinformatics tools.
News Item First ELIXIR.NO newsletter
 
News Item The Norwegian Bioinformatics Platform organizes the SocBiN Bioinformatics 2014 meeting
 
News Item The 2013 Galaxy Community Conference (GCC2013)
 
News Item ELIXIR.NO opening - Bergen, February 12, 2013
 
CourseNewsItem Course News: Extracting ecological signal from noise: introduction to tools for the analysis of NGS data from microbial communities, Bergen, April 19-20 2012
This intensive two-day course will provide an overview of AmpliconNoise and CREST - two important tools for the analysis of high throughput sequencing data from microbial communities.
CourseNewsItem Course News: Highthroughput data analysis course, Bergen, 21-23 March 2012
J-Express is an analysis suite for interpretation of high-throughput experiment data, commonly used for gene expression microarray analysis, but also applicable for other types of data.  
News Item BREW 2012 workshop for PhD students in bioinformatics - Announcement
 
CourseNewsItem Course News: Next-generation sequencing hands-on course: March 12-14
The Bioinformatics core facility and the Norwegian Microarray Consortium arrange an introductory hands-on course in bioinformatic analysis of next-generation sequencing data.
CourseNewsItem Course News: Introduction to high throughput genomics, Bergen, 01. -02. December 2011
An introductory course to the field of high troughput genomics such as microarray technology and high throughput sequencing.
CourseNewsItem Course News: Next-generation sequencing hands-on data analysis
The Bioinformatics core facility in Trondheim arranges an introductory hands-on course in bioinformatic analysis of next-generation sequencing data. The focus will be on short micro-RNA sequencing and ChIP-seq reads mapped to the human genome.
News Item Norwegian Sequencing Centre announces a course in basic HTS applications and bioinformatics, and a one-day seminar
 

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