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Keywords: Exploratory-analysis  or metagenomics  or HCI  or Chip-seq  or Cells and Organisms 


Chip-seq: Motif Analysis Tutorial

Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, Motif analysis, NGS, Pattern recognition

Chip-seq: Motif Analysis Tutorial https://tess.elixir-europe.org/materials/chip-seq-motif-analysis-tutorial Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, Motif analysis, NGS, Pattern recognition
Chip-seq: Functional Annotation tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Chip-seq, Functional Annotation, NGS

Chip-seq: Functional Annotation tutorial https://tess.elixir-europe.org/materials/chip-seq-functional-annotation-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Chip-seq, Functional Annotation, NGS
Introducing Bivi.co

Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations

Resource type: Video

Introducing Bivi.co https://tess.elixir-europe.org/materials/introducing-bivi-co Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting. Created at: 1st BiVi Annual Meeting. Prof. Jessie Kennedy Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations 2016-12-08
Biological Networks

Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction...

Scientific topics: Pathway or network

Keywords: Cells and Organisms, Pathway

Resource type: Video

Biological Networks https://tess.elixir-europe.org/materials/biological-networks Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction networks.(PLEASE NOTE: There is a small formatting problem with the presentation slides for the first 2 min of the talk only). This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Dr. Scooter Morris Pathway or network Cells and Organisms, Pathway 2017-01-31
Keynote on Visual Design Principles

Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure...

Keywords: Genome, HCI, Information visualisation, Communication

Resource type: Video

Keynote on Visual Design Principles https://tess.elixir-europe.org/materials/keynote-on-visual-design-principles Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure design.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Martin Krzywinski Genome, HCI, Information visualisation, Communication 2017-01-31
Cellular Image Data

Peter Sorger (http://sorger.med.harvard.edu/) and Bang Wong (http://bang.clearscience.info/) talk about the challenges of visualising large sets of multidimensional data (e.g. single cell imaging, dose-response assays, multiplex biochemistry etc.).This video was filmed and distributed with...

Keywords: Cells and Organisms

Resource type: Video

Cellular Image Data https://tess.elixir-europe.org/materials/cellular-image-data Peter Sorger (http://sorger.med.harvard.edu/) and Bang Wong (http://bang.clearscience.info/) talk about the challenges of visualising large sets of multidimensional data (e.g. single cell imaging, dose-response assays, multiplex biochemistry etc.).This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Bang Wong Cells and Organisms 2017-01-31
Infectious Disease Host/Pathogen Relationships

Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance...

Keywords: Populations, HCI

Resource type: Video

Infectious Disease Host/Pathogen Relationships https://tess.elixir-europe.org/materials/infectious-disease-host-pathogen-relationships Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance of human-computer interface professionals in the design process.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Populations, HCI 2017-01-31
BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

BBSRC: Data and Data Visualisation https://tess.elixir-europe.org/materials/bbsrc-data-and-data-visualisation Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Michael Ball Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation 2017-02-01
Cell lineage visualisation

Dr A J Pretorius discusses Cell-o-pane, a cell lineage visulaisation tool at 1st BiVi in 2014. As assoicated poster also presented a the meeting is included. Created at: 1st BiVi Annual Meeting.

Keywords: Cells and Organisms, Molecular

Resource type: Video

Cell lineage visualisation https://tess.elixir-europe.org/materials/cell-lineage-visualisation Dr A J Pretorius discusses Cell-o-pane, a cell lineage visulaisation tool at 1st BiVi in 2014. As assoicated poster also presented a the meeting is included. Created at: 1st BiVi Annual Meeting. Dr. A.J. Pretorius Cells and Organisms, Molecular 2017-02-01
BioLayout Express 3D

Derek Wright discusses the BioLayout Express visualisation tool at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Cells and Organisms, Genome, Pathway

Resource type: Video

BioLayout Express 3D https://tess.elixir-europe.org/materials/biolayout-express-3d Derek Wright discusses the BioLayout Express visualisation tool at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Derek Wright Pathway or network Cells and Organisms, Genome, Pathway 2017-02-02
Revise and Redraw—Visual Design Principles for Scientific Data

Martin Krzywinski's keynote from 1st BiVi in 2014. He discusses visual design principles and communicating effectively in pictures.This talk distills core concepts of information design into practical guidelines for creating scientific figures. We will explain how to generate visual vocabularies...

Keywords: HCI, Communication

Resource type: Video

Revise and Redraw—Visual Design Principles for Scientific Data https://tess.elixir-europe.org/materials/revise-and-redraw-visual-design-principles-for-scientific-data Martin Krzywinski's keynote from 1st BiVi in 2014. He discusses visual design principles and communicating effectively in pictures.This talk distills core concepts of information design into practical guidelines for creating scientific figures. We will explain how to generate visual vocabularies with graphical elements, combine them into phrases, and package them into a complete figure, the visual equivalent of a paragraph. We show how effective designs for this composition are underpinned by conclusions from studies in visual perception and awareness. Created at: 1st BiVi Annual Meeting. Martin Krzywinski HCI, Communication 2017-02-02
Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees

Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool. Created at: 1st BiVi Annual Meeting.

Keywords: Genome, Populations, HCI

Resource type: Poster

Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees https://tess.elixir-europe.org/materials/evaluation-of-helium-visualisation-of-large-scale-plant-pedigrees Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool. Created at: 1st BiVi Annual Meeting. Dr. Paul Shaw Genome, Populations, HCI 2017-02-02
Zegami: A tool for image data exploration

Stephen Taylor discusses the Zegami visualisation tool at 1st BiVi in 2014. An associated poster is also available. Created at: 1st BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome

Resource type: Poster, Video

Zegami: A tool for image data exploration https://tess.elixir-europe.org/materials/zegami-a-tool-for-image-data-exploration Stephen Taylor discusses the Zegami visualisation tool at 1st BiVi in 2014. An associated poster is also available. Created at: 1st BiVi Annual Meeting. Stephen Taylor Anatomy Physiology and Atlases, Cells and Organisms, Genome 2017-02-02
Zegami: Image visualisation, annotation and searching

Stephen Taylor describes and demonstrates Zegami at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome

Resource type: Slideshow

Zegami: Image visualisation, annotation and searching https://tess.elixir-europe.org/materials/zegami-image-visualisation-annotation-and-searching Stephen Taylor describes and demonstrates Zegami at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Stephen Taylor Anatomy Physiology and Atlases, Cells and Organisms, Genome 2017-02-03
Art and Science: A partnership catalyzing discovery in biomedicine

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine https://tess.elixir-europe.org/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicine A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science. Created at: 3rd BiVi Annual Meeting (2017). Bang Wong Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation 2017-05-12
Zegami: Digital Data Integration, Visualisation and Management

Stephen Taylor discusses Zegami with examples and latest developments at 3rd BiVi in April 2017.Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated...

Scientific topics: Database management

Keywords: Cells and Organisms, Databases

Resource type: Video

Zegami: Digital Data Integration, Visualisation and Management https://tess.elixir-europe.org/materials/zegami-digital-data-integration-visualisation-and-management Stephen Taylor discusses Zegami with examples and latest developments at 3rd BiVi in April 2017.Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated metadata) on a massive scale allowing querying and organisation of large image based collections. The talk will show various examples of its usage in biology and beyond, and will look at new features such as annotation to build training sets for machine learning. Created at: 3rd BiVi Annual Meeting (2017). Stephen Taylor Database management Cells and Organisms, Databases 2017-05-12
Model organism analysis using Intermine

Poster presented at 3rd BiVi in April 2017.InterMine is an open source data warehouse based in the University of Cambridge. We integrate data from disparate sources and provide a single unified interface, allowing you to access your data via an easy-to-use webapp or API. InterMine has over 30...

Keywords: Cells and Organisms

Resource type: Poster

Model organism analysis using Intermine https://tess.elixir-europe.org/materials/model-organism-analysis-using-intermine Poster presented at 3rd BiVi in April 2017.InterMine is an open source data warehouse based in the University of Cambridge. We integrate data from disparate sources and provide a single unified interface, allowing you to access your data via an easy-to-use webapp or API. InterMine has over 30 different instances worldwide, covering model organisms, plants, mitochondrial DNA, drug targeting, and more.  Created at: 3rd BiVi Annual Meeting (2017). Ms. Yo Yehudi Cells and Organisms 2017-05-30
Chip-seq: Pattern Analysis tutorial

Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, NGS, Pattern recognition

Chip-seq: Pattern Analysis tutorial https://tess.elixir-europe.org/materials/chip-seq-pattern-analysis-tutorial Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, NGS, Pattern recognition
Chip-seq: Peak calling tutorial

The aim is to : Understand how to process reads to obtain peaks (peak-calling). Become familiar with differential analysis of peaks In practice : Obtain dataset from GEO Analyze mapped reads Obtain set(s) of peaks, handle replicates Differential analysis of peak

Keywords: Chip-seq, NGS, Peak calling

Chip-seq: Peak calling tutorial https://tess.elixir-europe.org/materials/chip-seq-peak-calling-tutorial The aim is to : Understand how to process reads to obtain peaks (peak-calling). Become familiar with differential analysis of peaks In practice : Obtain dataset from GEO Analyze mapped reads Obtain set(s) of peaks, handle replicates Differential analysis of peak Chip-seq, NGS, Peak calling
Chip Seq: Annotation and visualization Lesson

How to add biological meaning to peaks

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Lesson https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-lesson How to add biological meaning to peaks Annotation, Chip-seq, Data Visualization, NGS
Chip-seq Analysis

Quality, normalisation and peak calling

Keywords: Chip-seq, Genomics

Chip-seq Analysis https://tess.elixir-europe.org/materials/chip-seq-analysis Quality, normalisation and peak calling Chip-seq, Genomics
Chip Seq: Annotation and visualization Tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Tutorial https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Annotation, Chip-seq, Data Visualization, NGS
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

Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses https://tess.elixir-europe.org/materials/who-is-doing-what-on-the-cheese-surface-overview-of-the-cheese-microbial-ecosystem-functioning-by-metatranscriptomic-analyses-55c4b5d0-ba6e-4ae0-879f-7bc27c10b3eb 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 long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We used an iterative sensory procedure to select a simplified microbial consortium, composed of only nine species (three yeasts and six bacteria), producing the odor of Livarot-type cheese when inoculated in a sterile cheese curd. All the genomes were sequenced in order to determine the functional capacities of the different species and facilitate RNA-Seq data analyses. We followed the ripening process of experimental cheeses made using this consortium during four weeks, by metatranscriptomic and biochemical analyses. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. We next applied the same approach to investigate the activity of the microorganisms in real cheeses, namely Reblochon-style cheeses. This provided useful insights into the physiological changes that occur during cheese ripening, such as changes in energy substrates, anabolic reactions, or stresses. metagenomics 2016-12-15 2017-01-11
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

Soil metagenomics, potential and pitfalls https://tess.elixir-europe.org/materials/soil-metagenomics-potential-and-pitfalls-04d3bb46-36ba-47c0-9993-9c7d0aacad32 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). Nevertheless, genome structure information has been restricted by a large extent to a small fraction of cultivated species. This limitation can be circumvented now by modern alternative approaches including metagenomics or single cell genomics. Metagenomics includes the data treatment of DNA sequences from many members of the microbial community, in order to either extract a specific microorganism’s genome sequence or to evaluate the community function based on the relative quantities of different gene families. In my talk I will show how these metagenomic datasets can be used to estimate and compare the functional potential of microbial communities from various environments with a special focus on antibiotic resistance genes. However, metagenomic datasets can also in some cases be partially assembled into longer sequences representing microbial genetic structures for trying to correlate different functions to their co-location on the same genetic structure. I will show how the microbial community composition of a natural grassland soil characterized by extremely high microbial diversity could be managed for sequentially attempt to reconstruct some bacterial genomes. Metagenomics can also be used to exploit the genetic potential of environmental microorganisms. I will present an integrative approach coupling rrs phylochip and high throughput shotgun sequencing to investigate the shift in bacterial community structure and functions after incubation with chitin. In a second step, these functions of potential industrial interest can be discovered by using hybridization of soil metagenomic DNA clones spotted on high density membranes by a mix of oligonucleotide probes designed to target genes encoding for these enzymes. After affiliation of the positive hybridizing spots to the corresponding clones in the metagenomic library the inserts are sequenced, DNA assembled and annotated leading to identify new coding DNA sequences related to genes of interest with a good coverage but a low similarity against closest hits in the databases confirming novelty of the detected and cloned genes. metagenomics 2016-12-16 2017-01-11
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

Sequencing 6000 chloroplast genomes : the PhyloAlps project https://tess.elixir-europe.org/materials/sequencing-6000-chloroplast-genomes-the-phyloalps-project-a2b30d75-061a-4663-a5b8-593842df23bf 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 initiative, phylogeneticists often prefer markers with better phylogenic properties, and ecologists, with the coming of the DNA metabarcoding, look for a third class of markers easiest to amplify from environmental DNA. Nevertheless they have all the same need of the knowledge accumulated by the others. But having different markers means that the sequecences have been got from different individuals in differente lab, following various protocoles. On that base, building a clean reference database, merging for each species all the available markers becomes a challenge. With the phyloAlps project we implement genome skimming at a large scale and propose it as a new way to set up such universal reference database usable by taxonomists, phylogeneticists, and ecologists. The Phyloalps project is producing for each species of the Alpine flora at least a genome skim composed of six millions of 100bp sequence reads. From such data it is simple to extract all chloroplastic, mitochondrial and nuclear rDNA markers commonely used. Moreover, most of the time we can get access to the complete chloroplast genome sequence and to a shallow sequencing of many nuclear genes. This methodes have already been successfully applied to algeae, insects and others animals. With the new single cell sequencing methods it will be applicable to most of the unicellular organisms. The good question is now : Can we consider the genome skimming as the next-generation DNA barcode ? metagenomics 2016-12-16 2017-01-11
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

From Samples to Data : Assuring Downstream Analysis with Upstream Planning https://tess.elixir-europe.org/materials/from-samples-to-data-assuring-downstream-analysis-with-upstream-planning-6fac0f49-b453-4c15-a409-9753fb27ee9b 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 this powerful technology depends on sample preparation, library construction and the selection of appropriate sequencing technology and sequencing depth. Here we explore the different variables involved in the process of preparing samples for sequencing analysis including sample collection, DNA extraction and library construction. We also examine the various sequencing technologies deployed for routine metagenomic analysis and considerations for their use in different model systems including humans, mouse and the environment. Future developments such as long-reads will also be discussed to provide a complete picture of important aspects prior to data analyses which play a critical role in the success of metagenomic studies. metagenomics 2017-01-11
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

Revealing and analyzing microbial networks: from topology to functional behaviors https://tess.elixir-europe.org/materials/revealing-and-analyzing-microbial-networks-from-topology-to-functional-behaviors-14d83c7f-c5f9-4738-8cd5-42e48a1088f7 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 task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete. Within this seminar, we will illustrate two complementary approaches that aim to overcome these points in different manners. metagenomics 2016-12-16 2017-01-11
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

Reconstructing genomes from metagenomes: The holy grail of microbiology https://tess.elixir-europe.org/materials/reconstructing-genomes-from-metagenomes-the-holy-grail-of-microbiology-be78338f-13ef-40d6-92cf-621fbccf8808 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 about the organization of genes in cognate genomes. Several factors affect the assembly performance, and the feasibility of the assembly-based approaches varies across environments. However, increasing read lengths, novel experimental approaches, advances in computational tools and resources, and improvements in assembly algorithms and pipelines render the assembly-based metagenomic workflow more and more accessible. The utility of metagenomic assembly remarkably increases when contigs are organized into metagenome-assembled genomes (MAGs). Often-novel MAGs frequently provide deeper insights into bacterial lifestyles that would otherwise remain unknown as evidenced by recent discoveries. The increasing rate of the recovery of MAGs presents new opportunities to link environmental distribution patterns of microbial populations and their functional potential, and transforms the field of microbiology by providing a more complete understanding of the microbial life, ecology, and evolution. metagenomics 2016-12-16 2017-01-11
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

Rationale and Tools to look for the unknown in (metagenomic) sequence data https://tess.elixir-europe.org/materials/rationale-and-tools-to-look-for-the-unknown-in-metagenomic-sequence-data-5dd1e1a8-6db2-4b78-b1fc-60e1a5fbcee8 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. When exploring beyond the frontier of known biology, one should expect a large proportion of environmental sequences not exhibiting any significant similarity with known organisms. Notably, this is the case for eukaryotic viruses belonging to new families, for which the proportion of "no match" could reach 90%. Most metagenomics studies tend to ignore this large fraction of sequences that might be the equivalent of "black matter" in Biology. We will present some of the ideas and tools we are using to extract that information from large metagenomics data sets in search of truly unknown microorganisms. One of the tools, "Seqtinizer", an interactive contig selection/inspection interface will also be presented in the context of "pseudo-metagenomic" projects, where the main organism under genomic study (such as sponges or corals) turns out to be (highly) mixed with an unexpected population of food, passing-by, or symbiotic microorganisms. metagenomics 2016-12-16 2017-01-11
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

Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification https://tess.elixir-europe.org/materials/prokaryotic-phylogeny-on-the-fly-databases-and-tools-for-online-taxonomic-identification-84732559-32a2-4c4c-9c94-2bd3c3773717 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 into different subsets using phylogenetic information. The procedure for computing a phylogeny is completely automated. Homologous sequence are first recruited through a BLAST search performed on a sequence (or a set of sequences). Then the homologous sequences detected are aligned using one of the multiple sequence alignment programs provided in the pipeline (MAFFT, MUSCLE or CLUSTALO). The alignment is then filtered using BMGE and a Maximum Likelihood (ML) tree is computed using the program FastTree. The tree can be rooted with an outgroup provided by the user and its leaves are coloured with a scheme related to the taxonomy of the sequences. The main advantage provided by PPF is that its databases are generated using a phylogeny-oriented procedure and and therefore much more efficient for phylogentic analyses that "generic" collections such as SILVA (in the case SSU rRNA) por GenBank. It is therefore much more suited to compute prokaryotic molecular phylogenies than related systems such as the Phylogeny.fr online system. PPF can be accessed online at https://umr5558-bibiserv.univ-lyon1.fr/lebibi/PPF-in.cgi metagenomics 2016-12-16 2017-01-11