Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=40&ordering=-dateCreation
{ "count": 149, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=60&ordering=-dateCreation", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=20&ordering=-dateCreation", "results": [ { "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": 111, "name": "Chip-seq: Discovering motifs in peaks with RSAT", "description": "Read mapping: from raw reads to aligned reads.\nPeak calling: from aligned reads to regions/peaks of high read density.\nChIP-seq annotation\nIdentification of genes related to the peaks.\nProfiles of ChIP-seq reads around reference points (TSS, histone marks,).\nFunctional enrichment of the genes related to the peaks.\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/ChIP-seq_motifs_EBA2015_JvH.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Motif analysis", "Chip Seq", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?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": 125, "name": "ETBII 2023", "description": "All the training materials dedicated to the IFB's Integrative Bioinformatics Thematic School, which took place in January 2023.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://moodle.france-bioinformatique.fr/course/view.php?id=13", "fileName": "ETBII 2023 Training materials", "topics": [ "http://edamontology.org/topic_3474", "http://edamontology.org/topic_3316", "http://edamontology.org/topic_3391", "http://edamontology.org/topic_3365", "http://edamontology.org/topic_0092", "http://edamontology.org/topic_2269", "http://edamontology.org/topic_0091", "http://edamontology.org/topic_3307" ], "keywords": [ "Biological network inference and analysis", "Multivariate analyses", "Semantic web", "Data Integration" ], "audienceTypes": [ "Professional (initial)" ], "audienceRoles": [ "Life scientists", "Computer scientists", "Bioinformaticians" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 29, "name": "IFB Core", "url": "https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/762/?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": 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": 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": 49, "name": "Development in Galaxy", "description": "Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/galaxyproject/training-material/tree/master/Dev-Corner", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/77/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?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" ] }, { "id": 128, "name": "Mapping with Galaxy", "description": "This tutorial covers the questions:\r\n- What is mapping?\r\n- What two things are crucial for a correct mapping?\r\n- What is BAM?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Define what mapping is\r\n- Perform mapping of reads on a reference genome\r\n- Evaluate the mapping output", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html", "fileName": "mapping", "topics": [ "http://edamontology.org/topic_0102" ], "keywords": [ "Mapping" ], "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": 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": 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": 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": 1, "name": "SG-ONT-slides", "description": "Slides used for the training \"\t\r\nIntroduction to Oxford Nanopore Technology data analyses\"", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://southgreenplatform.github.io/trainings//files/ont_2021.pdf", "fileName": "ont_2021.pdf", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2022-01-24", "dateUpdate": "2022-01-24", "licence": "Creative Commons Attribution 4.0 International License", "maintainers": [] }, { "id": 15, "name": "From Biotea to Bioschemas: definition of profiles required to represent scholarly publications", "description": "\n \n\nFrom Biotea to Bioschemas: definition of profiles required to represent scholarly publications\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/from-biotea-to-bioschemas_28f9/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/678/?format=api" ] }, { "id": 29, "name": "Adding bioschemas markup to data repository", "description": "\n \n\nAdding bioschemas markup to data repository\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/adding-bioschemas_8b91/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "biohackaton" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2019-03-21", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/688/?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": 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": 14, "name": "Galaxy training material improvement and extension", "description": "\n \n\nGalaxy training material improvement and extension\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/galaxy-training-material_6300/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/677/?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" ] } ] }