Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=60&ordering=-name
{ "count": 144, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=80&ordering=-name", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=40&ordering=-name", "results": [ { "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": 145, "name": "Introduction to Transcriptomics", "description": "This slidedecks presents the concepts behind transcriptomics", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/introduction/slides.html", "fileName": "transcriptomics-introduction", "topics": [ "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_3170" ], "keywords": [ "RNA-seq", "Transcriptomics (RNA-seq)" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 142, "name": "Introduction to python", "description": "Training slides (theory and exercises)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training-python-for-biology-genotoul-bioinfo-a77c191514cdd1dc1b.pages.mia.inra.fr/#/title-slide", "fileName": "training-python-for-biology", "topics": [ "http://edamontology.org/topic_3316" ], "keywords": [ "Python Language" ], "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Life scientists" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "Creative Commons Attribution 4.0 International License", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 133, "name": "Introduction to image analysis using Galaxy", "description": "This tutorial covers the questions:\r\n- How do I use Galaxy with imaging data?\r\n- How do I convert images using Galaxy?\r\n- How do I display images in Galaxy?\r\n- How do I filter images in Galaxy?\r\n- How do I segment simple images in Galaxy?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- How to handle images in Galaxy.\r\n- How to perform basic image processing in Galaxy.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html", "fileName": "imaging-introduction", "topics": [ "http://edamontology.org/topic_3383", "http://edamontology.org/topic_3382" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 120, "name": "Initiation to Galaxy", "description": "DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/GALAXY-TP-INITIATION-Roscoff-Septembre2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "DNA Analysis", "Variant calling", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 11, "name": "Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment", "description": "\n \n\nImprove Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/improve-shiny-and-rstudio_fcd3/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/362/?format=api" ] }, { "id": 12, "name": "Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits", "description": "\n \n\nImprove Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/improve-orphanet_8da2/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/675/?format=api" ] }, { "id": 13, "name": "Import workflows into TeSS Concept Maps", "description": "\n \n\nImport workflows into TeSS Concept Maps\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/import-workflows-into-tess_4062/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/676/?format=api" ] }, { "id": 123, "name": "IFB Cloud tutorial: Gene regulation", "description": "1. Using the Gene-regulation appliance\n1.1 Requirements\n1.2 Virtual disk creation\n1.3 Creation of an instance\n1.4 Connection to the device\n1.5 Download source data\n1.6 Execute workflow\n\n2. Visualizing results\n2.1 Install and run the X2Go client on your host computer\n2.2 Visualize results\nFastQC\nIGV\n\n\n3. Create your own Gene-regulation appliance\nCreation of an instance\nInstalling programs and dependencies\nGet the gene-regulation repository\nRun makefile to install the dependencies\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/rioualen/gene-regulation/blob/master/doc/gene-regulation_tutorials/gene-regulation_with_IFB_cloud.Rmd", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Cloud Computing" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-05-31", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?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": 71, "name": "Holistic metagenomics in marine communities", "description": "Complex microscopic communities are composed of species belonging to all life realms, from single-cell prokaryotes to multicellular eukaryotes of small size. Each component of a community needs to be studied for a full understanding of the functions performed by the whole assemblage, however methods to investigate microbiomes are generally restricted to a single kingdom. Using examples from the Tara Oceans project, we will show how size fractionation and use of varied metabarcoding, metagenomics and metatranscriptomics approaches can help studying the marine plankton community as a whole, in a wide geographic space.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_7/Holistic_metagenomics_in_marine_communities/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/702/?format=api" ] }, { "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/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/123/?format=api" ] }, { "id": 86, "name": "Gut metagenomics in cardiometabolic diseases", "description": "Cardio-metabolic and Nutrition-related diseases (CMDs) represent an enormous burden for health care. They are characterized by very heterogeneous phenotypes progressing with time. It is virtually impossible to predict who will or will not develop cardiovascular comorbidities. There is a clear need to intervene earlier in the natural cycle of the disease, before irreversible tissue damages develop. Predictive tools still remain elusive and environmental factors (food, nutrition, physical activity and psychosocial factors) play major roles in the development of these interrelated pathologies. Poor nutritional environment and lifestyle also promote health deterioration resulting in CMD progression. In the last few years, the characterization of the gut microbiome (i.e. collective bacteria genome) and gut-derived molecules (i.e. metabolites, lipids, inflammatory molecules) has opened up new avenues for the generation of fundamental knowledge regarding putative shared pathways in CMD. The gut microbiome is likely to have an even greater impact than genetic factors given its close relationship with environmental factors. In metabolic disorders, the discoveries that low bacterial gene richness associates with cardiovascular risks stimulate encourage these developments. Due to the complexity of the gut microbiome, and its interactions with human (host) metabolism as well as with the immune system, it is only through integrative analyses where metabolic network models are used as scaffold for analysis that it will be possible to identify markers and shared pathways, which will contribute to improve patient stratification and develop new modes of patient care.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_2/Gut_metagenomics_in_cardiometabolic_diseases/scormcontent/index.html", "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/712/?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": 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": 44, "name": "Galaxy Visualisation - Tutorial", "description": "Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in settings like zooming in and assigning colors, etc. Therefore, visualizations are ideally interactive, and changing settings is often an initial step in exploring data. For this reason it may be inconvenient to make use of static galaxy tools because it lacks these interactive features. For these situations Galaxy offers the option to create visualizations plugins, file format specific javascripts that integrate with the history menu, without making redundant copies of data.\nIn this tutorial we shall go through how this system works and create a simple visualization plugin. The tool will create a visualization of the number of aligned reads per chromosome of a BAM file, and we will discuss possible optimizations and advantages and disadvantages of the proposed implementation.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/tutorials/visualizations", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/690/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/691/?format=api" ] }, { "id": 45, "name": "Galaxy Visualisation - Slides", "description": "Questions\n\n\n\tHow can visualization plugins benefit science?\n\n\n\nObjectives\n\n\n\tImplement a first Galaxy visualization\n\tUnderstand the client side vs. server side principle\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/visualizations.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/690/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/691/?format=api" ] }, { "id": 14, "name": "Galaxy training material improvement and extension", "description": "\n \n\nGalaxy training material improvement and extension\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/galaxy-training-material_6300/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/677/?format=api" ] }, { "id": 43, "name": "Galaxy Interactive Tour", "description": "Questions\nWhat is a Galaxy Interactive Tour?\nHow to create a Galaxy Interactive Tour?\nObjectives\nDiscover what is a Galaxy Interactive Tour\nBe able to create a Galaxy Interactive Tour\nBe able to add a Galaxy Interactive Tour in a Galaxy instance\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/interactive_tour.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api" ] }, { "id": 42, "name": "Galaxy Installation", "description": "How to install a local instance of Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/00-installation/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" ] } ] }