Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=120&ordering=topics
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Samples are then either submitted as new entries or updated if they already exist in the database.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://forgemia.inra.fr/urgi-is/data-brokering", "fileName": "submit_data_biosamples_X.py", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "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", "https://catalogue.france-bioinformatique.fr/api/userprofile/813/?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/187/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/59/?format=api" ] }, { "id": 35, "name": "Defining and importing genomes, Data Managers into Galaxy", "description": "Intro to built in datasets\nBuilt in data hierarchy\nSome problems\nData Managers\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/07-genomes-datamanagers/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": 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": 9, "name": "OmicsPath: Finding Relevant omics datasets using pathway information", "description": "\n \n\nOmicsPath: Finding Relevant omics datasets using pathway information\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/omicspath-finding_b649/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/673/?format=api" ] }, { "id": 118, "name": "Chip-seq: Introduction to the Workshop", "description": "Data visualization, quality control, normalization & peak calling\nPeak annotation\nFrom peaks to motifs\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/slides/chipseq_CarlHerrmann_Roscoff2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/661/?format=api" ] }, { "id": 88, "name": "From Samples to Data : Assuring Downstream Analysis with Upstream Planning", "description": "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.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_1/From_Samples_to_Data_Assuring_Downstream_Analysis_with_Upstream_Planning/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/714/?format=api" ] }, { "id": 7, "name": "Prototyping the new PSICQUIC 2-0", "description": "\n \n\nPrototyping the new PSICQUIC 2.0\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/prototyping_353b/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/671/?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": 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": 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": 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": 82, "name": "Sequencing 6000 chloroplast genomes : the PhyloAlps project", "description": "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 ?\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_3/Sequencing_6000_chloroplast_genomes_the_PhyloAlps_project/scormcontent/", "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/126/?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": 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": 136, "name": "Training RNASeq - biostat part - Genotoul-bioinfo", "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", "https://catalogue.france-bioinformatique.fr/api/userprofile/739/?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": 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": 93, "name": "Cross Taxa Tutorial", "description": "How query databases according to complex taxonomic critera\nCross-Taxa allows to retrieve gene families that are shared by a given set of taxa, or which are specific to a set of taxa. It is also possible to select genes families which are associated to a certain set of taxa but which are not found in a second set of taxa. Any taxonomic level can be used.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article41", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/715/?format=api" ] } ] }