{"count":149,"next":null,"previous":"https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=json&limit=20&offset=120&ordering=difficultyLevel","results":[{"id":138,"name":"Linux TP - Genotoul-bioinfo","description":"TP for linux training (genotoul bioinfo facility)\r\nThis training session on one day (09:00 / 17 :00) is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your workstation, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://genotoul-bioinfo.pages-forge.inrae.fr/linux-cluster/","fileName":"linux-cluster","topics":["http://edamontology.org/topic_3316"],"keywords":["Operating systems"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Novice","providedBy":[],"dateCreation":null,"dateUpdate":null,"licence":"CC BY-NC-SA","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/739/?format=json"]},{"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_3391","http://edamontology.org/topic_3365","http://edamontology.org/topic_3307","http://edamontology.org/topic_2269","http://edamontology.org/topic_3316","http://edamontology.org/topic_0092","http://edamontology.org/topic_0091","http://edamontology.org/topic_3474"],"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=json"}],"dateCreation":null,"dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=json"]},{"id":132,"name":"Metatranscriptomics analysis using microbiome RNA-seq data","description":"This tutorial covers the questions:\r\n- How to analyze metatranscriptomics data?\r\n- What information can be extracted of metatranscriptomics data?\r\n- How to assign taxa and function to the identified sequences?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Choose the best approach to analyze metatranscriptomics data\r\n- Understand the functional microbiome characterization using metatranscriptomic results\r\n- Understand where metatranscriptomics fits in ‘multi-omic’ analysis of microbiomes\r\n- Visualise a community structure","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics/tutorial.html","fileName":"metatranscriptomics","topics":["http://edamontology.org/topic_1775","http://edamontology.org/topic_3941"],"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=json"]},{"id":137,"name":"Linux slides - Genotoul-bioinfo","description":"Slides for linux session (genotoul bioinfo facility)\r\nThis training session on one day (09:00 / 17 :00) is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your workstation, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://bioinfo.genotoul.fr/wp-content/uploads/Formation_LINUX_GenoToul_2025.pdf","fileName":"Formation_LINUX_GenoToul_2025.pdf","topics":["http://edamontology.org/topic_3316"],"keywords":["Operating systems"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Novice","providedBy":[],"dateCreation":null,"dateUpdate":null,"licence":"CC BY-NC-SA","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/739/?format=json"]},{"id":128,"name":"Mapping with Galaxy","description":"This tutorial covers the questions:\r\n- What is mapping?\r\n- What two things are crucial for a correct mapping?\r\n- What is BAM?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Define what mapping is\r\n- Perform mapping of reads on a reference genome\r\n- Evaluate the mapping output","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html","fileName":"mapping","topics":["http://edamontology.org/topic_0102"],"keywords":["Mapping"],"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=json"]},{"id":127,"name":"Quality Control with Galaxy","description":"This tutorial covers the questions:\r\n- How to perform quality control of NGS raw data?\r\n- What are the quality parameters to check for a dataset?\r\n- How to improve the quality of a dataset?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC\r\n- Assess long reads FASTQ quality using Nanoplot and PycoQC\r\n- Perform quality correction with Cutadapt (short reads)\r\n-  Summarise quality metrics MultiQC\r\n- Process single-end and paired-end data","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html","fileName":"quality-control","topics":["http://edamontology.org/topic_0091","http://edamontology.org/topic_3168"],"keywords":["Quality Control"],"audienceTypes":["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=json"]},{"id":129,"name":"Bacterial Genome Annotation","description":"This tutorial covers the questions:\r\n- Which genes are on a draft bacterial genome?\r\n- Which other genomic components can be found on a draft bacterial genome?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Run a series of tools to annotate a draft bacterial genome for different types of genomic components\r\n- Evaluate the annotation\r\n- Process the outputs to format them for visualization needs\r\n- Visualize a draft bacterial genome and its annotations","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html","fileName":"bacterial-genome-annotation","topics":["http://edamontology.org/topic_3301","http://edamontology.org/topic_0219"],"keywords":["Bacterial isolate","Annotation","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=json"]},{"id":130,"name":"Taxonomic Profiling and Visualization of Metagenomic Data","description":"This tutorial covers the questions:\r\n- Which species (or genera, families, …) are present in my sample?\r\n- What are the different approaches and tools to get the community profile of my sample?\r\n- How can we visualize and compare community profiles?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Explain what taxonomic assignment is\r\n- Explain how taxonomic assignment works\r\n- Apply Kraken and MetaPhlAn to assign taxonomic labels\r\n- Apply Krona and Pavian to visualize results of assignment and understand the output\r\n- Identify taxonomic classification tool that fits best depending on their data","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html","fileName":"taxonomic-profiling","topics":["http://edamontology.org/topic_3697","http://edamontology.org/topic_0637","http://edamontology.org/topic_3174"],"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=json"]},{"id":131,"name":"16S Microbial Analysis with mothur","description":"This tutorial covers the questions:\r\n- What is the effect of normal variation in the gut microbiome on host health?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy\r\n- Using a mock community to assess the error rate of your sequencing experiment\r\n- Visualize sample diversity using Krona and Phinch","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html","fileName":"mothur-miseq-sop-short","topics":["http://edamontology.org/topic_3697","http://edamontology.org/topic_0637"],"keywords":["Galaxy","Metabarcoding"],"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=json"]}]}