Training Material List
Handles creating, reading and updating training materials.
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"https://catalogue.france-bioinformatique.fr/api/userprofile/668/?format=api" ] }, { "id": 130, "name": "Taxonomic Profiling and Visualization of Metagenomic Data", "description": "This tutorial covers the questions:\r\n- Which species (or genera, families, …) are present in my sample?\r\n- What are the different approaches and tools to get the community profile of my sample?\r\n- How can we visualize and compare community profiles?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Explain what taxonomic assignment is\r\n- Explain how taxonomic assignment works\r\n- Apply Kraken and MetaPhlAn to assign taxonomic labels\r\n- Apply Krona and Pavian to visualize results of assignment and understand the output\r\n- Identify taxonomic classification tool that fits best depending on their data", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html", "fileName": "taxonomic-profiling", "topics": [ "http://edamontology.org/topic_3697", "http://edamontology.org/topic_3174", "http://edamontology.org/topic_0637" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 121, "name": "The IFB cloud for bioinformatics", "description": "\n\tPractical work to introduce basic and advanced usage of the IFB cloud\nHowto launch virtual machines\nManaging your data in the cloud ;\nHowto to connect to your VMS (SSH, web, remote desktop)\nPersonalizing your VMs (approver, galaxy, docker)\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/ekorpela/cloud-vm-workshop/blob/master/materials/IFBcloud/IFB%20cloud%20training%20ELIX-FI.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Cloud Computing", "Virtual machine" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-06-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/59/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?format=api" ] }, { "id": 68, "name": "Third generation sequencing : the revolution of long reads", "description": "Introduction on sequencing: available technologies, library types, applications ...\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://www.france-bioinformatique.fr/sites/default/files/I02_Thermes_ROSCOFF5.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-21", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/699/?format=api" ] }, { "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": 47, "name": "ToolShed upload and tool-iuc PR", "description": "Questions\nWhat is a Tool Shed?\nHow to install tools and workflows from a Tool Shed into a Galaxy instance?\nWhat are the Tool Shed repository types?\nHow to publish with Planemo?\nObjectives\nDiscover what is a Tool Shed\nBe able to install tools and workflows from a Tool Shed into a Galaxy instance\nBe able to publish tools with Planemo\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day2/toolshed/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-17", "dateUpdate": null, "licence": null, "maintainers": [ "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": 140, "name": "TP Cluster", "description": "TP for cluster training (bioinfo genotoul facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/linux-cluster/", "fileName": "linux-cluster", "topics": [], "keywords": [ "Cluster" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 141, "name": "training material sed and awk training", "description": "training material sed and awk training (genotoul bioinfo facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genoweb.toulouse.inra.fr/~klopp/SedAwk2024/Processing_large_files_with_sed_awk_2024.pdf", "fileName": "Processing_large_files_with_sed_awk_2024.pdf", "topics": [ "http://edamontology.org/topic_3316" ], "keywords": [ "Programming Languages & Computer Sciences" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "Creative Commons Attribution 4.0 International License", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 96, "name": "Training 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_Formation.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": 135, "name": "training RNASEQ Bioinfo part", "description": "Cette formation a pour but de vous aider à traiter les séquences courtes issues des plates-formes de séquençage Illumina. Vous y découvrirez les formats de séquences et d’alignement les biais connus et mettrez en œuvre des logiciels d'alignement épissé sur génome de référence, la recherche de nouveaux gènes, de nouveaux transcrits et la quantification de l'expression de ces gènes et transcrits.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/training-rnaseq", "fileName": "training-rnaseq", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 136, "name": "training RNASeq biostat part", "description": "This course is part of the INRAE training session about “bioinformatics and biostatistics analysis of RNA-seq data” and of the Biostatistics platform “Initiation à LA statistique, niveau 4”. \r\nThe material provided on the present webpage is related to the biostatistics part and covers the following topics:\r\n\r\nR and RStudio\r\ndesign of experiments\r\nvariability\r\ncount data normalization\r\ndifferential analysis\r\nThe material has originally been prepared by Ignacio Gonzales, Annick Moisan and myself. The class has already been taught by these persons but also by Gaëlle Lefort and Jérôme Mariette.\r\n\r\nPre-requisites: A background in R programming is necessary for this class. Before the class, please download the course material and install R, RStudio and the packages as described below. To produce high quality figures, I will use ggplot2 for plots but will not enter into details about the ggplot2 syntax. If you are not familiar with it, you can just use these command lines or switch to base plots instead.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://www.nathalievialaneix.eu/teaching/rnaseq.html", "fileName": "rnaseq.html", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 54, "name": "Transcriptome de novo assembly", "description": "Not available\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/A01_Galaxy_RNASeq_denovo_ITMO2016_0.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/134/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/388/?format=api" ] }, { "id": 3, "name": "Transfer of Research Assets between FAIRDOM SEEKs", "description": "\n \n\nTransfer of Research Assets between FAIRDOM SEEKs\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/transfer-of-research_9014/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/667/?format=api" ] }, { "id": 34, "name": "Users, Groups, and Quotas in Galaxy", "description": "How to handle Users, Groups, and Quotas in Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/08-quota-users-groups/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api" ] }, { "id": 2, "name": "Using blockchain in biomedical provenance, the identifiers use case", "description": "\n \n\nUsing blockchain in biomedical provenance, the identifiers use case\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/using-blockchain_039d/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/666/?format=api" ] }, { "id": 59, "name": "Variant annotation", "description": "Add meta-information on variant to facilitate interpretation\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/V06_variants_annotation.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Variant analysis" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/693/?format=api" ] }, { "id": 63, "name": "Variant Filtering", "description": "Use cases:\nExtact a subset of variants\nCombine variants from several analysis\n\nCompare obtained variants from several data types\n\n\nIdentify new variants compare to a reference list\n\n\nApply specific filters for Chip Design\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/FiltrageVariantNLapaluRoscoff2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Variant calling", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/694/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/719/?format=api" ] }, { "id": 64, "name": "Variants: alignment and pre-treatment; GATK", "description": "DNA-seq Bioinformatics Analysis: from raw sequences to processed alignments\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/V01_ITMO_2016_EG_from_fastq_to_mapping_1.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "DNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/256/?format=api" ] }, { "id": 119, "name": "Visualization of NGS data with IGV", "description": "Visualisation of next-gen sequencing data with Integrative Genomics Viewer\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/IGV-Roscoff-Septembre2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Data visualization", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "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": [] } ] }