Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=40&ordering=maintainers
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Seq de novo", "description": "\n \n\nPractical session on transciptome de novo assembly\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/A01b_Galaxy_RNASeq_denovo_ITMO2016_TP_v2red.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/134/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/388/?format=api" ] }, { "id": 46, "name": "BioBlend API", "description": "BioBlend module, a python library to use Galaxy API\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/bioblend_api.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy", "Python", "API" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/189/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/414/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/563/?format=api" ] }, { "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": 30, "name": "Welcome message", "description": "Presentation of the workshop (Chairman: Claudine Médigue)\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_1/welcome_message/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics", "biohackaton" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-15", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/664/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/431/?format=api" ] }, { "id": 22, "name": "CWL support in Galaxy", "description": "\n \n\nCWL support in Galaxy\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/cwl-support-in-galaxy_f872/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/432/?format=api" ] }, { "id": 150, "name": "Plant Data Managment for Phenotyping Experiments - MIAPPE", "description": "The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org) has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking between phenotype and genotype datasets, relevant section of MIAPPE are beginning to be used for genotyping standards. This Webinar will give an overview of the current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity inherent to research and breeding data sets. Data management approaches at some of the major research organizations will be given as examples.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://hal.inrae.fr/hal-03102944", "fileName": "2020-12-MIAPPE-Webinar.pdf", "topics": [ "http://edamontology.org/topic_0625" ], "keywords": [ "Données" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-SA 4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/441/?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": 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": 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" ] }, { "id": 55, "name": "x2Go", "description": "Opening an x2go session to the IFBcloud\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/x2go_to_IFB-VM.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Cloud" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 65, "name": "Chip-seq Analysis", "description": "Quality, normalisation and peak calling\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/C01_ChIP_SEQ_EBA_2016-11-22.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Chip-Seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/695/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/696/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/697/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?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": 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, 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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" ] } ] }