Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=100&ordering=-topics
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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 be associated to known organisms. On the other hand, de novo methods, that compare the whole set of sequences, do not scale up on ambitious metagenomic projects.\nThese limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecology distances by replacing species counts by k-mer counts. Simka scales-up today metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets.\nExperiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecology distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_4/Multiple_comparative_metagenomics_using_multiset_k_mer_couting/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/708/?format=api" ] }, { "id": 110, "name": "DNA-seq analysis: From raw reads to processed alignments", "description": "Objectives:\nMapping the DNA-seq data to the reference genome\nProcess the alignments for the variant calling\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/elodie_girard-itmo2015_mapping_preprocess.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Variant calling", "Alignment", "DNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/256/?format=api" ] }, { "id": 99, "name": " PASTEClassifier Tutorial", "description": "The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 )\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://urgi.versailles.inra.fr/Tools/PASTEClassifier/PASTEClassifier-tuto", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Transposons" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CeCILL", "maintainers": [] }, { "id": 48, "name": "Tool development and integration into Galaxy", "description": "Questions:\nWhat is a tool for Galaxy?\nHow to build a tool/wrapper with the good practices?\nHow to deal with the tool environment?\n \nObjectives:\nDiscover what is a wrapper and its structure\nUse the Planemo utilities to develop a good wrapper\nDeal with the dependencies\nWrite functional tests\nMake a tool ready for publishing in a ToolShed\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/tool_integration.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-16", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/663/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 28, "name": "Alternative episodes for the 4 Open Source Software", "description": "\n \n\nAlternative episodes for the 4 Open Source Software (4OSS) lesson focused on different Open Source technologies: Github, Docker, Jupyter Notebook and so on\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/alternative-episodes_8b36/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "biohackaton 2018" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2019-03-21", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/687/?format=api" ] }, { "id": 94, "name": "Searching for sequence: Tutorial", "description": "Quick Search is dedicated to a quick search for sequences or sequence families in the databases available on the PBIL server. It is an alternative to WWW Query which allows more complex queries. Quick Search allows you to retrieve sequences or sequence families associated to a single word without specifying what is this word. You can enter indifferently a keyword, a sequence name or accession number, or a taxa name.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article17", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Pattern recognition" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/715/?format=api" ] }, { "id": 30, "name": "Welcome message", "description": "Presentation of the workshop (Chairman: Claudine Médigue)\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_1/welcome_message/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics", "biohackaton" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-15", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/664/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/431/?format=api" ] }, { "id": 95, "name": "Exercices on Galaxy: metagenomics", "description": "Find Rapidly OTU with Galaxy Solution\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://genoweb.toulouse.inra.fr/~formation/15_FROGS/April2016/FROGS_april_2016_Pratice.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/215/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/716/?format=api" ] }, { "id": 122, "name": "Docker tutorial: Gene regulation", "description": "Get started with Docker!\nCreate a Docker account\nInstall Docker on your local host\nCreate shared repositories and download source data\nFetch the Docker image and run it with shared folders\nExecute the pipeline\n\nJVH / Mac\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/rioualen/gene-regulation/blob/master/doc/gene-regulation_tutorials/gene-regulation_with_docker.Rmd", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Docker" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-05-31", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 62, "name": "RNA-seq: Differential gene expression analysis", "description": "Transcriptome analysis provides information about the identity and quantity of all RNA molecules\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R01_EBA206_RNAseq_ref.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/371/?format=api" ] }, { "id": 117, "name": "Chip-seq: Peak calling tutorial", "description": "The aim is to :\nUnderstand how to process reads to obtain peaks (peak-calling).\nBecome familiar with differential analysis of peaks\nIn practice :\nObtain dataset from GEO\nAnalyze mapped reads\nObtain set(s) of peaks, handle replicates\nDifferential analysis of peak\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/01_peak_calling/peak_calling_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Peak calling", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/721/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 97, "name": "Analysis of community composition data using phyloseq", "description": "Learn about and become familiar with phyloseq R package for the analysis of microbial census data\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://genoweb.toulouse.inra.fr/~formation/15_FROGS/April2016/R_phyloseq/phyloseq_formation_toulouse_201604.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "R", "Microbiomes" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/717/?format=api" ] }, { "id": 114, "name": "Chip Seq: Annotation and visualization Lesson", "description": "How to add biological meaning to peaks\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/slides/ChIP-seq_annotation_MD_2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Data visualization", "Annotation", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/720/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 126, "name": "Galaxy 101 for everyone", "description": "This practical aims at familiarizing you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows and sharing your work. Not everyone has the same background and that’s ok!", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html", "fileName": "galaxy-intro-101-everyone", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 67, "name": "Galaxy: Initiation II", "description": "Galaxy II: common tools, quality control; alignment; data managment\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/G045_16-11-21-galaxy-tp-initiation-II-0.3.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-21", "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 50, "name": "Welcome and Introduction", "description": "\n \n\nIntroduction message of the EGDW 2017\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://ressources.france-bioinformatique.fr/sites/default/files/introduction.pdf", "fileName": " introduction.pdf", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-16", "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 51, "name": "Eukaryotic small RNA", "description": "\n \n\nSmall RNAseq data analysis for miRNA identification\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/sRNA-Seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/642/?format=api" ] }, { "id": 76, "name": " Reconstructing genomes from metagenomes: The holy grail of microbiology", "description": "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.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_5/Reconstructing_genomes_from_metagenomes_the_holy_grail_of_microbiology/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/665/?format=api" ] } ] }