Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=120&ordering=licence
{ "count": 149, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=140&ordering=licence", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=100&ordering=licence", "results": [ { "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": 124, "name": "Snakemake tutorial: Gene regulation", "description": "Workflow 1: Rules and targets\nWorkflow 2: Introducing wildcards\nWorkflow 3: Keywords\nWorkflow 4: Combining rules\nWorkflow 5: Configuration file\nWorkflow 6: Separated files\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://gene-regulation.readthedocs.io/en/latest/snakemake.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Snakemake" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-13", "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": 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_0092", "http://edamontology.org/topic_2269", "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": 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": 5, "name": "Putting structured data into individual entry pages in biological database", "description": "\n \n\nPutting structured data into individual entry pages in biological database\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/putting-structured_bf31/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/669/?format=api" ] }, { "id": 4, "name": "Support tools for rapid adoption of compact identifiers in the publishing process", "description": "\n \n\nSupport tools for rapid adoption of compact identifiers in the publishing process\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/support-tools_78a0/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/668/?format=api" ] }, { "id": 3, "name": "Transfer of Research Assets between FAIRDOM SEEKs", "description": "\n \n\nTransfer of Research Assets between FAIRDOM SEEKs\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/transfer-of-research_9014/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/667/?format=api" ] }, { "id": 148, "name": "One line perl", "description": "Improve your command line skills by learning a few words of Perl (08/12/2025)\r\nThe GenoToul bioinformatics platform and Sigenae organize a series of training courses to familiarize yourself with the various resources it provides. These resources are currently: the hardware infrastructure, biological data banks and widely used bioinformatics softwares. This “Perl one-liners” training session is organized by the Sigenae platform. Perl one-liners are small and awesome Perl programs that fit in a single line of code and perform many operations such as replacing of text, spacing, deleting, calculation, manipulation in files and many more. This training will allow you to discover the power of Perl on the command line and learn how to use it to automate your file manipulations and command line generation with classical file formats such as tabulated text, fastq, sam/bam, and vcf.\r\n\r\ncalendar\r\n \r\n\r\nThis training lasts one day and is focused on practice. It consists of 3 parts with a large variety of exercises:\r\n\r\nIntroduction to Perl and its characteristics: Perl is a widely used programming language for data processing and task automation. We will introduce the main characteristics of Perl and discuss why it is particularly suited for biologists who want to manipulate files and generate command lines.\r\nPerl on the command line: we will show how to use Perl on the command line to perform common tasks, such as searching and replacing strings, merging files, and loop over lists of files.\r\nConcrete examples: we will present several concrete examples drawn from biology, such as extracting information from genomic sequence files, converting files between different formats, and generating command lines for data biology tools.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://web-genobioinfo.toulouse.inrae.fr/~ccabau/Perl_One-liner.pdf", "fileName": "Perl_One-liner.pdf", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 2, "name": "Using blockchain in biomedical provenance, the identifiers use case", "description": "\n \n\nUsing blockchain in biomedical provenance, the identifiers use case\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/using-blockchain_039d/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/666/?format=api" ] }, { "id": 146, "name": "Processing_large_files_with_sed_awk_2024", "description": "This “Sed and AWK to modify large text files” training session is organized by the Genotoul bioinfo platform.\r\n\r\nThe Linux sed command is a powerful and very fast text editor without an interface. Sed can select, substitute, add, delete, and modify text in files and streams. Sed relies heavily on regular expressions for pattern matching and text selection. We’ll manipulate regexes and the sed command to modify and filter several type of file often used in bioinformatics.\r\n\r\nAWK enables to easily process columns in large text files but is also a quite powerfull programming language. This training session aims at introducing you AWK principles. You will learn about variables, operators and functions useful to manipulate very large files. \r\n\r\nFor example you can use AWK to generate your unix command lines to be launched on the cluster. AWK enables to process millions of lines in text files. The course includes short feature presentations between long hands-on sessions in which you will be able to understand the global ideas as well as details.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://web-genobioinfo.toulouse.inrae.fr/~klopp/SedAwk2024/Processing_large_files_with_sed_awk_2024.pdf", "fileName": "Processing_large_files_with_sed_awk_2024.pdf", "topics": [], "keywords": [], "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Biologists", "Bioinformaticians" ], "difficultyLevel": "Intermediate", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": "2024-03-01", "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?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" ] }, { "id": 135, "name": "training RNASEQ Bioinfo part", "description": "Cette formation a pour but de vous aider à traiter les séquences courtes issues des plates-formes de séquençage Illumina. Vous y découvrirez les formats de séquences et d’alignement les biais connus et mettrez en œuvre des logiciels d'alignement épissé sur génome de référence, la recherche de nouveaux gènes, de nouveaux transcrits et la quantification de l'expression de ces gènes et transcrits.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/training-rnaseq", "fileName": "training-rnaseq", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 136, "name": "training RNASeq biostat part", "description": "This course is part of the INRAE training session about “bioinformatics and biostatistics analysis of RNA-seq data” and of the Biostatistics platform “Initiation à LA statistique, niveau 4”. \r\nThe material provided on the present webpage is related to the biostatistics part and covers the following topics:\r\n\r\nR and RStudio\r\ndesign of experiments\r\nvariability\r\ncount data normalization\r\ndifferential analysis\r\nThe material has originally been prepared by Ignacio Gonzales, Annick Moisan and myself. The class has already been taught by these persons but also by Gaëlle Lefort and Jérôme Mariette.\r\n\r\nPre-requisites: A background in R programming is necessary for this class. Before the class, please download the course material and install R, RStudio and the packages as described below. To produce high quality figures, I will use ggplot2 for plots but will not enter into details about the ggplot2 syntax. If you are not familiar with it, you can just use these command lines or switch to base plots instead.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://www.nathalievialaneix.eu/teaching/rnaseq.html", "fileName": "rnaseq.html", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?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": 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": 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": 38, "name": "(Proxy) Web Server Choices and Configuration", "description": "Installation and configuration of NGiNX for Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/04-web-server/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy", "NGiNX" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api" ] }, { "id": 39, "name": "Galaxy Handlers", "description": "Galaxy is a web application that uses handlers to perform actions.\nThere are two main types of actions that are carried out by handlers:\nRespond to user requests; These actions are carried out by web handlers\nManage the execution of tools; These actions are performed by job handlers.\nBy default, Galaxy is configured to run a single handler that handles both user queries and jobs.\nDepending on the number of users accessing your Galaxy instance or the number of jobs you need to manage you may need to start web handlers or additional job handlers.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/03-handlers/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": 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" ] } ] }