Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=20&ordering=-audienceRoles
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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": 39, "name": "Galaxy Handlers", "description": "Galaxy is a web application that uses handlers to perform actions.\nThere are two main types of actions that are carried out by handlers:\nRespond to user requests; These actions are carried out by web handlers\nManage the execution of tools; These actions are performed by job handlers.\nBy default, Galaxy is configured to run a single handler that handles both user queries and jobs.\nDepending on the number of users accessing your Galaxy instance or the number of jobs you need to manage you may need to start web handlers or additional job handlers.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/03-handlers/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/563/?format=api" ] }, { "id": 27, "name": "Application of RDF-based models and tools for enhancing interoperable", "description": "\n \n\nApplication of RDF-based models and tools for enhancing interoperable use of biomedical resources\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/application-of-rdf_8aed/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/686/?format=api" ] }, { "id": 26, "name": "Assessing the FAIRness of Training Materials", "description": "\n \n\nAssessing the FAIRness of Training Materials\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/assessing-the-ffairness_8da7/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/685/?format=api" ] }, { "id": 137, "name": "Linux slides", "description": "Slides for linux session (genotoul bioinfo facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation_LINUX_GenoToul_2024.pdf", "fileName": "Formation_LINUX_GenoToul_2024.pdf", "topics": [], "keywords": [ "Operating systems" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?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": 33, "name": "Docker for Beginners", "description": "What is Docker?\nBuilding an image\nBioShadock & Orchestration\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://vdda.github.io/revealJS_test/docker_intro2.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Docker" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?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": 57, "name": "DNA - seq Bioinformatics Analysis", "description": "Detection of Copy Number Variations\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/V07_ITMO_2016_EG_CNV.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "DNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/256/?format=api" ] }, { "id": 109, "name": "RNA-Seq: Differential Expression Analysis", "description": "\n \n\nBe careful about experimental design : avoid putting all the\nreplicates in the same lane, using the same barcode for the\nreplicates, putting different number of samples in lanes etc...\nNon- uniformity of the per base read distribution (Illumina Random\nHexamer Priming bias visible on the 13 first bases)\nBias hierarchy : biological condition >> concentration > run/flowcell> lane\nAt equivalent expression level, a long gene will have more reads than a short one.\nNon random coverage along the transcript.\nMultiple hit for some reads alignments.\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://ressources.france-bioinformatique.fr/sites/default/files/EBA/V4-2015/RNAseq/billerey-roscoff_expr_diff_tp-vfinal.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Differential Expression", "RNA-seq", "Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/55/?format=api" ] }, { "id": 149, "name": "Supports FAIR data PLANT PHENO 2023", "description": "Ensemble des supports utilisés pour la version 2023 de la formation FAIR data PLANT PHENO", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://moodle.france-bioinformatique.fr/course/view.php?id=17", "fileName": "Supports FAIR data PLANT PHENO 2023", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [ { "id": 26, "name": "URGI", "url": "https://catalogue.france-bioinformatique.fr/api/team/URGI/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/441/?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": 20, "name": "Development of a catalog of federated SPARQL queries in the field of Rare Diseases", "description": "\n \n\nDevelopment of a catalog of federated SPARQL queries in the field of Rare Diseases\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/development-of-a-catalog_f08f/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/292/?format=api" ] }, { "id": 25, "name": "Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)", "description": "\n \n\nBioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/bioconda-packaging_e168/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/624/?format=api" ] }, { "id": 101, "name": "REPET: TEdenovo tutorial", "description": "The TEdenovo pipeline follows a philosophy in three first steps:\nDetection of repeated sequences (potential TE)\nClustering of these sequences\nGeneration of consensus sequences for each cluster, representing the ancestral TE\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CeCILL", "maintainers": [] }, { "id": 10, "name": "JSON schema validation with ontologies", "description": "\n \n\nJSON schema validation with ontologies\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/json-schema-validation_deb6/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/674/?format=api" ] }, { "id": 106, "name": "Genomic copy number Tutorial", "description": "We will analyze the copy number variations of a human tumor (parotid gland carcinoma), limited to the chr17, from a WES (whole-exome sequencing) experiment. All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37).\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/CNV_TD_guidelines_BJ.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Structural genomics", "Copy number" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 120, "name": "Initiation to Galaxy", "description": "DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/GALAXY-TP-INITIATION-Roscoff-Septembre2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "DNA Analysis", "Variant calling", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 151, "name": "Metagenomic training", "description": "Slides and link to practical session parts", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation2025.pdf", "fileName": "Formation2025.pdf", "topics": [ "http://edamontology.org/topic_3174" ], "keywords": [], "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": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 77, "name": "Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification", "description": "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\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_5/Procaryotic_phylogenu_on_the_fly/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/489/?format=api" ] } ] }