BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection).  They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with  (ODC-By) v1.0 license.

Either as a cooperation or consultancy service.

A comprehensive enzyme information system. It is the world’s largest and most widely information system on all aspects of enzymes, including function, structure, mutants, properties like stability, purification. Data download is possible as an integrated text filed or via SOAP.

ELIXIR-NL can help organise standard events that make data sources more FAIR by applying Linked Data, or help make data repository software more FAIR. Such meetings focus on one or two data sources, and will bring together your experts on the data content and on the usage of the data with experts in data modeling. As an important side-effect such events also educate the participants on what it means to make data FAIR in practice.

Either as a cooperation or consultancy service.

contact [at] denbi.de

Expertise includes

• DNA microarray
• RNA‐Seq
• qPCR processing pipelines
• array‐CGH, SNP
• NGS data analysis

Either as a cooperation or consultancy service.

contact [at] denbi.de

Dissemination events: 

• Seminars / Webinars 
• Workshops
• Events for high-schools

Online environment to learn to code based on automatic feedback on the submissions of programming exercises

For analysis of high-throughput sequencing incorporating many tools, training, literature and guides

The GTPB runs face-to-face Bioinformatics Training Courses regularly at the Instituto Gulbenkian de Ciência.

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

A web tool and a mobile app for exploring the entire Tree of Life

A compilation of tools offering identification and quantification of microorganisms, working with cellular pathways, phylogenetic trees and microbial communities, including: 

• MOCAT - a modular and scalable software pipeline for analyzing shotgun metagenomics datasets generated with Illumina technology. 
• mOTUs - Metagenomic operational taxonomic units (mOTUs) allow for the quantification of known (sequenced) and unknown microorganisms at species-level resolution from shotgun sequencing data. 
• SIAMCAT -  a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. 
• eggNOG - a database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. 
• Enterotyping - uses computational methods to detect and characterise densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. 
• iPATH - a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. 
• iTOL - Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. 

MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.

Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity.

Annotation of plant reference genomes and pangenomes, support and consulting.

A capacity building and training programme in data management for the life sciences

A training materials portal that helps you to discover, package and disseminate training resources. It aggregates training information from the ELIXIR nodes, and also from third-party content providers.

Interdisciplinary trainings in post‐genome technologies and computation

Training events about tools developed in ELIXIR-EE (usually g:Profiler, MEM, ClustVis are taught).

Courses in bioinformatics and HPC at CSC are open for academics, government and industry participants.

• Bioinformatics tools and resources
• Computational skills
• (bio)data science
• Data management, annotation and analysis
• Data interoperability and FAIRification
• bio.tools and Bioschemas

Training provided by ELIXIR-LU focuses on the usage of the Node services, data management, efficient use of high-performance computing to analyse complex biomedical data, and reproducibility in research.

Most of the training organised in DTL/ELIXIR-NL and the associated Dutch research school on bioinformatics and systems biology (BioSB) are open to participants from any ELIXIR country. Training and training materials available are listed on dtls.nl and TeSS. Training and materials are developed on a diverse range of topics, including specific bioinformatics skills and workflows, as well as generic FAIR data knowledge and data stewardship.

SIB Training offers courses and workshops on various bioinformatics and data science-related fields to life scientists, clinicians and bioinformaticians. 

Courses providing fundamental data skills for research, basic skills for research computing, and knowledge for research data management and ELIXIR Belgium’s Node Services.

The ELIXIR UK training centres include Cambridge Bioinformatics Training Centre, University of Cambridge, Edinburgh Genomics and Birmingham Metabolomics Training Centre.

Either as a cooperation or consultancy service.

Either as a cooperation or consultancy service.

contact [at] denbi.de