Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=60&ordering=-description
{ "count": 144, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=80&ordering=-description", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=40&ordering=-description", "results": [ { "id": 6, "name": "ProtVista (protein annotation viewer) extension using Bioschemas data", "description": "\n \n\nProtVista (protein annotation viewer) extension using Bioschemas data\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/protvista-protein_2cd8/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/670/?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": 37, "name": "Connecting Galaxy to a compute cluster", "description": "Problems\nRunning jobs on the Galaxy server negatively impacts Galaxy UI performance\nEven adding one other host helps\nCan restart Galaxy without interrupting jobs\nSolution:\nConnecter Galaxy to a computing cluster\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/05-compute-cluster/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy", "Cluster" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?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": 121, "name": "The IFB cloud for bioinformatics", "description": "\n\tPractical work to introduce basic and advanced usage of the IFB cloud\nHowto launch virtual machines\nManaging your data in the cloud ;\nHowto to connect to your VMS (SSH, web, remote desktop)\nPersonalizing your VMs (approver, galaxy, docker)\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/ekorpela/cloud-vm-workshop/blob/master/materials/IFBcloud/IFB%20cloud%20training%20ELIX-FI.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Cloud Computing", "Virtual machine" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-06-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/59/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?format=api" ] }, { "id": 53, "name": "RNA - 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/388/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/134/?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": 8, "name": "Pathway effect prediction for protein targets", "description": "\n \n\nPathway effect prediction for protein targets\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/pathway-effect_b1e2/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/672/?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": 9, "name": "OmicsPath: Finding Relevant omics datasets using pathway information", "description": "\n \n\nOmicsPath: Finding Relevant omics datasets using pathway information\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/omicspath-finding_b649/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/673/?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": 58, "name": "Isoform discovery and quanti cation from RNA-Seq data", "description": "Not available\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R04_EBA2016_RNAseq_Isoforms.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/605/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/159/?format=api" ] }, { "id": 54, "name": "Transcriptome de novo assembly", "description": "Not available\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/A01_Galaxy_RNASeq_denovo_ITMO2016_0.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/134/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/388/?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": 74, "name": " MG-RAST - experiences from processing a quarter million metagenomic data sets", "description": "MG-RAST has been offering metagenomic analyses since 2007. Over 20,000 researchers have submitted data. I will describe the current MG-RAST implementation and demonstrate some of its capabilities. In the course of the presentation I will highlight several metagenomic pitfalls. MG-RAST: http://metagenomics.anl.gov MG-RAST-APP: http://api.metagenomics.anl.gov/api.html\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_6/MG_RSAT/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/705/?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": 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": 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": 80, "name": "Multiple Comparative Metagenomics using Multiset k-mer Counting", "description": "Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole set of sequences, do not scale up on ambitious metagenomic projects.\nThese limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecology distances by replacing species counts by k-mer counts. Simka scales-up today metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets.\nExperiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecology distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_4/Multiple_comparative_metagenomics_using_multiset_k_mer_couting/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/708/?format=api" ] }, { "id": 10, "name": "JSON schema validation with ontologies", "description": "\n \n\nJSON schema validation with ontologies\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/json-schema-validation_deb6/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/674/?format=api" ] } ] }