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  • IFB French Institute of Bioinformatics

    The French Institute of Bioinformatics (CNRS IFB) is a national service infrastructure in...

    138 training materials
    3 upcoming events (412 past events)
    IFB French Institute of Bioinformatics https://tess.elixir-europe.org/content_providers/ifb-french-institute-of-bioinformatics The French Institute of Bioinformatics (CNRS IFB) is a national service infrastructure in bioinformatics. IFB’s principal mission is to provide basic services and resources in bioinformatics for scientists and engineers working in the life sciences. IFB is the French node of the European research infrastructure, ELIXIR. /system/content_providers/images/000/000/049/original/logo-ifb-couleur.svg?1663599376
  • Showing 30 materials out of 138. View all results.
    200 billion sequences and counting: analysis, discovery and exploration of datasets with EBI Metagenomics

    EBI metagenomics (EMG, https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of...

    Keywords: metagenomics

    Assessing microbial biogeography by using a metagenomic approach

    Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors...

    Keywords: metagenomics

    Deciphering the human intestinal tract microbiome using metagenomic computational methods

    In 2010, the MetaHIT consortium published a 3.3M microbiota gene catalog generated by whole genome shotgun metagenomic sequencing, representing a mixture of bacteria, archaea, parasites and viruses coming from 124 human stool metagenomic samples [Qin et al, Nature 2010].
    However most of the genes...

    Keywords: metagenomics

    Dr Jekyll and Mr Hyde: The dual face of metagenomics in phylogenetic analysis

    The aim of this lecture is to present the impact of metagenomics and single-cell genomics on public databases. These new powerful approches allow us to have access to the diversity of life on our planet. However, care has to be taken when using these data for posterior analyses, such as...

    Keywords: metagenomics

    Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities

    Meta3C is an experimental and computational approach that exploits the physical contacts experienced by DNA molecules sharing the same cellular compartments. These collisions provide a quantitativeinformation that allows interpreting and phasing the genomes present within complex mixes of species...

    Keywords: metagenomics

    Fast filtering, mapping and assembly of 16S ribosomal RNA

    The application of next-generation sequencing technologies to RNA orDNA directly extracted from a community of organisms yields a mixtureof nucleotide fragments. The task to distinguish amongst these and tofurther categorize the families of ribosomal RNAs (or any other givenmarker) is an...

    Keywords: metagenomics

    Gut metagenomics in cardiometabolic diseases

    Cardio-metabolic and Nutrition-related diseases (CMDs) represent an enormous burden for health care. They are characterized by very heterogeneous phenotypes progressing with time. It is virtually impossible to predict who will or will not develop cardiovascular comorbidities. There is a clear...

    Keywords: metagenomics

    Hidden in the permafrost

    The last decade witnessed the discovery of four families of giant viruses infecting Acanthamoeba. They have genome encoding from 500 to 2000 genes, a large fraction of which encoding proteins of unknown origin. These unique proteins meant to recognize and manipulate the same building blocks as...

    Keywords: metagenomics

    Holistic metagenomics in marine communities

    Complex microscopic communities are composed of species belonging to all life realms, from single-cell prokaryotes to multicellular eukaryotes of small size. Each component of a community needs to be studied for a full understanding of the functions performed by the whole assemblage, however...

    Keywords: metagenomics

    MG-RAST — experiences from processing a quarter million metagenomic data sets

    MG-RAST has been offering metagenomic analyses since 2007. Over 20,000 researchers have submitted data. I will describe the current MG-RAST implementation and demonstrate some of its capabilities. In the course of the presentation I will highlight several metagenomic pitfalls. MG-RAST:...

    Keywords: metagenomics

    Multiple Comparative Metagenomics using Multiset k-mer Counting

    Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can...

    Keywords: metagenomics

    New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology

    It is a generally accepted characteristic of the biogeochemical nitrogen cycle that nitrification is catalyzed by two distinct clades of microorganisms. First, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite, which subsequently is oxidized to nitrate by nitrite-oxidizing...

    Keywords: metagenomics

    Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification

    PPF (Prokaryotic Phylogeny on the Fly) is an automated pipeline allowing to compute molecular phylogenies for prokarotic organisms. It is based on a set of specialized databases devoted to SSU rRNA, the most commonly used marker for bacterial txonomic identification. Those databases are splitted...

    Keywords: metagenomics

    Rationale and Tools to look for the unknown in (metagenomic) sequence data

    The interpretation of metagenomic data (environmental, microbiome, etc, ...) usually involves the recognition of sequence similarity with previously identified (micro-organisms). This is for instance the main approach to taxonomical assignments and a starting point to most diversity analyses....

    Keywords: metagenomics

    Reconstructing genomes from metagenomes: The holy grail of microbiology

    Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information...

    Keywords: metagenomics

    Revealing and analyzing microbial networks: from topology to functional behaviors

    Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated...

    Keywords: metagenomics

    From Samples to Data : Assuring Downstream Analysis with Upstream Planning

    Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by...

    Keywords: metagenomics

    Sequencing 6000 chloroplast genomes : the PhyloAlps project

    Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding...

    Keywords: metagenomics

    Soil metagenomics, potential and pitfalls

    The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation)....

    Keywords: metagenomics

    Welcome message

    Presentation of the workshop (Chairman: Victoria Dominguez Del Angel)

    Keywords: biohackaton

    Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses

    Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a...

    Keywords: metagenomics

    (Proxy) Web Server Choices and Configuration

    Installation and configuration of NGiNX for Galaxy

    Keywords: Galaxy, NGiNX

    Galaxy Administration

    How to use the administation panel of Galaxy

    Keywords: Galaxy

    RADSeq Data Analysis

    Introduction to RADSeq through STACKS on Galaxy

    Keywords: NGS

    Galaxy Docker Training Tutorial

    Galaxy docker integration
    Enable Galaxy to use BioContainers (Docker)
    Galaxy with Docker swarm

    Keywords: Docker, Galaxy

    Defining and importing genomes, Data Managers into Galaxy

    Intro to built in datasets
    Built in data hierarchy
    Some problems
    Data Managers

    Keywords: Galaxy

    Galaxy III: Visualization

    Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV)

    Keywords: Genomics

    Users, Groups, and Quotas in Galaxy

    How to handle Users, Groups, and Quotas in Galaxy

    Keywords: Galaxy

    Connecting Galaxy to a compute cluster

    Problems
    Running jobs on the Galaxy server negatively impacts Galaxy UI performance
    Even adding one other host helps
    Can restart Galaxy without interrupting jobs
    Solution:
    Connecter Galaxy to a computing cluster

    Keywords: Cluster, Galaxy

    Galactic Database

    How to choose a database for Galaxy and configure it

    Keywords: Galaxy

    Showing 3 upcoming events. Found 412 past events. View all results.
    • LINUX - session 2022/10/10

      10 October 2022

      ELIXIR node event
    • 11ème Ecole de Bioinformatique AVIESAN-IFB-Inserm

      13 - 18 November 2022

      ELIXIR node event
    • Ecole Thématique de Bioinformatique Intégrative - session 2023 / Integrative Bioinforformatics training school - 2023 session

      16 - 20 January 2023

      ELIXIR node event