{"count":144,"next":"https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?limit=20&offset=20&ordering=maintainers","previous":null,"results":[{"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/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/187/"]},{"id":49,"name":"Development in Galaxy","description":"Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://github.com/galaxyproject/training-material/tree/master/Dev-Corner","fileName":"missing.txt","topics":[],"keywords":["Galaxy"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"","providedBy":[],"dateCreation":null,"dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/677/","https://catalogue.france-bioinformatique.fr/api/userprofile/77/","https://catalogue.france-bioinformatique.fr/api/userprofile/689/","https://catalogue.france-bioinformatique.fr/api/userprofile/362/"]},{"id":72,"name":"Hidden in the permafrost","description":"The last decade witnessed the discovery of four families of giant viruses infecting Acanthamoeba. They have genome encoding from 500 to 2000 genes, a large fraction of which encoding proteins of unknown origin. These unique proteins meant to recognize and manipulate the same building blocks as cells raise the question on their origin as well as the role viruses played in the cellular word evolution. The Mimiviridae and the Pandoraviridae are increasingly populated by members from very diverse habitats and are ubiquitous on the planet. After prospecting the space, we went back in the past and isolated two other giant virus families from a 30,000 years old permafrost sample, Pithovirus and Mollivirus sibericum. A metagenomics study of the sample was performed to inventory its biodiversity and assess to what extend the host and the viruses were dominant. I will describe the two sequencing approaches which have been used and compare the results.\n1: Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of Mimivirus. Science. 2004 Nov 19;306(5700):1344-50.\n2: Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science. 2013 Jul 19;341(6143):281-6. \n3: Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4274-9.\n4: Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5327-35.\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_7/Hidden_in_permafrost/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/703/","https://catalogue.france-bioinformatique.fr/api/userprofile/123/"]},{"id":83,"name":"Rationale and Tools to look for the unknown in (metagenomic) sequence data","description":"The interpretation of metagenomic data (environmental, microbiome, etc, ...) usually involves the recognition of sequence similarity with previously identified (micro-organisms). This is for instance the main approach to taxonomical assignments and a starting point to most diversity analyses. When exploring beyond the frontier of known biology, one should expect a large proportion of environmental sequences not exhibiting any significant similarity with known organisms. Notably, this is the case for eukaryotic viruses belonging to new families, for which the proportion of \"no match\" could reach 90%. Most metagenomics studies tend to ignore this large fraction of sequences that might be the equivalent of \"black matter\" in Biology. We will present some of the ideas and tools we are using to extract that information from large metagenomics data sets in search of truly unknown microorganisms.\nOne of the tools, \"Seqtinizer\", an interactive contig selection/inspection interface will also be presented in the context of \"pseudo-metagenomic\" projects, where the main organism under genomic study (such as sponges or corals) turns out to be (highly) mixed with an unexpected population of food, passing-by, or symbiotic microorganisms.\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_3/Rational_and_tools_to_look_for_the_unknown_in_sequence_data/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/123/"]},{"id":82,"name":"Sequencing 6000 chloroplast genomes : the PhyloAlps project","description":"Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding initiative, phylogeneticists often prefer markers with better phylogenic properties, and ecologists, with the coming of the DNA metabarcoding, look for a third class of markers easiest to amplify from environmental DNA. Nevertheless they have all the same need of the knowledge accumulated by the others. But having different markers means that the sequecences have been got from different individuals in differente lab, following various protocoles. On that base, building a clean reference database, merging for each species all the available markers becomes a challenge. With the phyloAlps project we implement genome skimming at a large  scale and propose it as a new way to set up such universal reference database usable by taxonomists, phylogeneticists, and ecologists. The Phyloalps project is producing for each species of the Alpine flora at least a genome skim composed of six millions of 100bp sequence reads. From such data it is simple to extract all chloroplastic, mitochondrial and nuclear rDNA markers commonely used. Moreover, most of the time we can get access to the complete chloroplast genome sequence and to a shallow sequencing of many nuclear genes. This methodes have already been successfully applied to algeae, insects and others animals. With the new single cell sequencing methods it will be applicable to most of the unicellular organisms. The good question is now : Can we consider the genome skimming as the next-generation DNA barcode ?\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_3/Sequencing_6000_chloroplast_genomes_the_PhyloAlps_project/scormcontent/","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/126/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/134/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/388/"]},{"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/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/605/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/159/"]},{"id":32,"name":"Docker and Galaxy","description":"Questions\nWhy Docker? What is it?\nHow to use Docker?\nHow to integrate Galaxy in Docker to facilitate its deployment?\nObjectives\nDocker basics\nGalaxy Docker image (usage)\nGalaxy Docker (internals)\nGalaxy flavours\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"http://galaxyproject.github.io/training-material//Admin-Corner/slides/galaxy_docker","fileName":"missing.txt","topics":[],"keywords":["Docker","Galaxy"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"","providedBy":[],"dateCreation":"2017-01-19","dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/663/","https://catalogue.france-bioinformatique.fr/api/userprofile/187/"]},{"id":33,"name":"Docker for Beginners","description":"What is Docker?\nBuilding an image\nBioShadock & Orchestration\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://vdda.github.io/revealJS_test/docker_intro2.html","fileName":"missing.txt","topics":[],"keywords":["Docker"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"","providedBy":[],"dateCreation":"2017-01-19","dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/187/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/664/","https://catalogue.france-bioinformatique.fr/api/userprofile/431/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/187/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/414/","https://catalogue.france-bioinformatique.fr/api/userprofile/563/"]},{"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/215/","https://catalogue.france-bioinformatique.fr/api/userprofile/716/"]},{"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/","https://catalogue.france-bioinformatique.fr/api/userprofile/716/"]},{"id":57,"name":"DNA - seq Bioinformatics Analysis","description":"Detection of Copy Number Variations\n \n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"http://www.france-bioinformatique.fr/sites/default/files/V07_ITMO_2016_EG_CNV.pdf","fileName":"missing.txt","topics":[],"keywords":["DNA-seq"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"","providedBy":[],"dateCreation":"2016-11-23","dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/256/"]},{"id":64,"name":"Variants: alignment and pre-treatment; GATK","description":"DNA-seq Bioinformatics Analysis: from raw sequences to processed alignments\n","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"http://www.france-bioinformatique.fr/sites/default/files/V01_ITMO_2016_EG_from_fastq_to_mapping_1.pdf","fileName":"missing.txt","topics":[],"keywords":["genomics","DNA-seq"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"","providedBy":[],"dateCreation":"2016-11-22","dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/256/"]}]}