Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=40&ordering=-id
{ "count": 149, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=60&ordering=-id", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=20&ordering=-id", "results": [ { "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": 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": 108, "name": "RNA-Seq: isoform detection and quantification", "description": "transcriptome from new condition\ntissue-speci c transcriptome\ndifferent development stages\ntranscriptome from non model organism\ncancer cell\nRNA maturation mutant\n \nHow to manage RNA-Seq data with genes subjected to di erential\nsplicing?\nIs it possible to discover new isoforms?\nIs it possible to quantify abundance of each isoform\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/toffano-TP_RNASeq_Isoform.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Isoforms", "RNA-seq", "Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/159/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/605/?format=api" ] }, { "id": 107, "name": "Genomic copy number Analysis", "description": "No description available\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/CNV_ROSCOFF_2015_BJ_20150930.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Structural genomics", "Copy number" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2015-09-10", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/318/?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": 105, "name": "Exploring Microscope Platform", "description": "\n \n\nHow to use the Microscope Platform to annotate and analyze microbial genomes.\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/Cours_MicroScope_mars2016_1-17.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation", "Sequence analysis", "Transcriptomics", "Microbial evolution", "Metabolomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-03-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/718/?format=api" ] }, { "id": 104, "name": "Exploring microbiomes with the MicroScope Platform", "description": "This module is separated in different courses:\nMicroScope: General overview, Keyword search and gene cart functionalities\n\n\n\n\n\n\n\n\n\n\n\n\nFunctional annotation of microbial genomes\n\n\n\n\n\n\n\n\nFunctional annotation of microbial genomes: Prediction of enzymatic functions\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: synteny\n\n\n\n\n\n\n\n\nAutomatic functional assignation and expert annotation of genes\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: phylogenetic profiles\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: pan-genome analysis\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: metabolic pathways\n\n\n\n\nSyntactic re-annotation of public microbial genomes\n\n\n\n\nSyntactic annotation of microbial genomes\n\n\n\n\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/Cours_MicroScope_mars2016_18-125.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation", "Transcriptomics", "Microbial evolution", "Metabolomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-03-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/718/?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": 100, "name": "REPET: TEdannot Tutorial", "description": "TEannot is able to annote a genome using DNA sequences library. 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": 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": 98, "name": "A Quick and focused overview of R data types and ggplot2 syntax", "description": "R and RStudio overview.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://genoweb.toulouse.inra.fr/~formation/15_FROGS/April2016/R_phyloseq/ModuleIntroInitR.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "R", "Statistics", "Graphical analysis" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/415/?format=api" ] }, { "id": 97, "name": "Analysis of community composition data using phyloseq", "description": "Learn about and become familiar with phyloseq R package for the analysis of microbial census data\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://genoweb.toulouse.inra.fr/~formation/15_FROGS/April2016/R_phyloseq/phyloseq_formation_toulouse_201604.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "R", "Microbiomes" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/717/?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/716/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/215/?format=api" ] }, { "id": 95, "name": "Exercices 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_Pratice.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/716/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/215/?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": 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": 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": 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": 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": [] } ] }