Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=80&ordering=-name
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It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows and sharing your work. Not everyone has the same background and that’s ok!", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html", "fileName": "galaxy-intro-101-everyone", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 40, "name": "Galactic Database", "description": "How to choose a database for Galaxy and configure it\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/02-database/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/563/?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": 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": 75, "name": "Fast filtering, mapping and assembly of 16S ribosomal RNA", "description": "The application of next-generation sequencing technologies to RNA or DNA directly extracted from a community of organisms yields a mixture of nucleotide fragments. The task to distinguish amongst these and to further categorize the families of ribosomal RNAs (or any other given marker) is an important step for examining the phylogenetic classification of the constituting species. In this perspective, we have developed a complete bioinformatics suite, called MATAM, capable of handling large sets of reads in a fast and accurate way. MATAM covers all steps of the analysis, from the identification of reads of interest in the raw sequencing data to the reconstruction of the full-length sequences of the marker and alignment to a reference database for taxonomic assignment. Part of MATAM is based on the SortMeRNA software, also developed by the team.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_6/Fast_filtering_mapping_and_assembly_of_16S_rRNA/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/610/?format=api" ] }, { "id": 16, "name": "Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships", "description": "\n \n\nExploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/exploring-pharmacogenomic_688a/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/140/?format=api" ] }, { "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": 85, "name": "Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities", "description": "Meta3C is an experimental and computational approach that exploits the physical contacts experienced by DNA molecules sharing the same cellular compartments. These collisions provide a quantitative information that allows interpreting and phasing the genomes present within complex mixes of species without prior knowledge. Not only the exploitation of chromosome physical 3D signatures hold interesting premises regarding solving the genome sequences from discrete species, but it also allows assigning mobile elements such as plasmids or phages to their hosts.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_2/Exploiting_collisions_between_DNA_molecules_to_characterize_the_genomic_structures_of_complex_communities/scormcontent/", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-15", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/711/?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/215/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/716/?format=api" ] }, { "id": 51, "name": "Eukaryotic small RNA", "description": "\n \n\nSmall RNAseq data analysis for miRNA identification\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/sRNA-Seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/642/?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_2269", "http://edamontology.org/topic_0092", "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": 17, "name": "Enrichment and propagation of metagenomic experimental metadata", "description": "\n \n\nEnrichment and propagation of metagenomic experimental metadata\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/enrichment-and-propagation_4418/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/679/?format=api" ] }, { "id": 78, "name": "Dr Jekyll and Mr Hyde: The dual face of metagenomics in phylogenetic analysis", "description": "The aim of this lecture is to present the impact of metagenomics and single-cell genomics on public databases. These new powerful approches allow us to have access to the diversity of life on our planet. However, care has to be taken when using these data for posterior analyses, such as phylogenetic studies, as critical errors can still be present in the databases. This course will incorporate examples taken from real studies, and we will investigate methods used for error detection.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_5/Dr_Jekyll_and_Mr_Hyde_The_dual_face_of_metagenomics_in_phylogenetic_analysis/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/706/?format=api" ] } ] }