Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&ordering=-maintainers
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This library can be a predicted TE library built by TEdenovo\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CeCILL", "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": 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": 90, "name": "A Simple Phylogenetic Tree Construction (part 2)", "description": "Understand the method used in identifying an unknown sequence.\nUnderstand the limitations of this method\nGet to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article60", "fileName": "missing.txt", "topics": [], "keywords": [ "Phylogenetics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [ { "id": 19, "name": "PRABI-AMSB", "url": "https://catalogue.france-bioinformatique.fr/api/team/PRABI-AMSB/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "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": 112, "name": "Chip-seq: Motif Analysis Tutorial", "description": "Introduction\nGoal\nThe aim is to :\nGet familiar with motif analysis of ChIP-seq data.\nLearn de novo motif discovery methods.\nIn practice :\nMotif discovery with peak-motifs\nDifferential analysis\nRandom controls\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/04_motif/motif_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Pattern recognition", "Motif analysis", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "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": 116, "name": "Chip-seq: Functional Annotation tutorial", "description": "Global Objective\nGiven a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/02_annotation/annotation.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Functional Annotation", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 91, "name": "A Simple Phylogenetic Tree Construction (part 1)", "description": "Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree.\nGet to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win).\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article59", "fileName": "missing.txt", "topics": [], "keywords": [ "Phylogenetics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [ { "id": 19, "name": "PRABI-AMSB", "url": "https://catalogue.france-bioinformatique.fr/api/team/PRABI-AMSB/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "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": 92, "name": "HOVERGEN tutorial", "description": "HOVERGEN is a database containing homologous vertebrate protein and nucleotide sequences. It allows to easily select similar gene sequences from a wide range of vertebrates. Hence it becomes particularly useful in comparative genomics, phylogeny and evolutionary studies on a molecular level. HOVERGEN Clean contains only complete sequences which reattach to their family. Hence its library is smaller, but more reliable.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article58", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "proteomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [ { "id": 19, "name": "PRABI-AMSB", "url": "https://catalogue.france-bioinformatique.fr/api/team/PRABI-AMSB/?format=api" } ], "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": 147, "name": "Data-brokering script", "description": "This project generates metadata in JSON-LD format for plant and animal biological samples and submits them to the European Nucleotide Archive (ENA)'s BioSamples database. The metadata is extracted from an Excel file and validated against the Plant MIAPPE checklist for plant samples and against the BioSamples minimal checklist for animal samples. 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": 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": 115, "name": "Chip-seq: Pattern Analysis tutorial", "description": "Goal\nThe aim is to :\nGet familiar with motif analysis of ChIP-seq data.\nLearn de novo motif discovery methods.\nIn practice :\nMotif discovery with peak-motifs\nDifferential analysis\nRandom controls\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/04_motif/motif_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Pattern recognition", "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/721/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?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": 113, "name": "Chip Seq: Annotation and visualization Tutorial", "description": "Global Objective\nGiven a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/02_annotation/annotation.html", "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": 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": [], 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"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" ] } ] }