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Content provider: CSC - IT Center for Science  or Bioschemas 


Introduction to using containers - OpenShift, Kubernetes and Docker oriented view

This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez

Keywords: Containers, Kubernetes, Cloud computing

Introduction to using containers - OpenShift, Kubernetes and Docker oriented view http://tess.elixir-uk.org/materials/introduction-to-using-containers-openshift-kubernetes-and-docker-oriented-view This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez Containers, Kubernetes, Cloud computing Cloud users
Schema.org, what and why?

In this tutorial you will get an idea on what Schema.org is and how it is useful

Keywords: schemaorg, markup, structured data, schemaorg, markup, structured data

Schema.org, what and why? http://tess.elixir-uk.org/materials/schema-org-what-and-why In this tutorial you will get an idea on what Schema.org is and how it is useful schemaorg, markup, structured data, schemaorg, markup, structured data
Bioschemas, what and why?

In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are

Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas

Bioschemas, what and why? http://tess.elixir-uk.org/materials/bioschemas-what-and-why In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Schema.org markup examples

With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup

Keywords: schemaorg, markup, structured data, example, schemaorg, markup, structured data, example

Schema.org markup examples http://tess.elixir-uk.org/materials/schema-org-markup-examples With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup schemaorg, markup, structured data, example, schemaorg, markup, structured data, example
How to select the right profile for your resource

In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources

Keywords: schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile

How to select the right profile for your resource http://tess.elixir-uk.org/materials/how-to-select-the-right-profile-for-your-resource In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile
How to update a profile

In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll.

Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile

How to update a profile http://tess.elixir-uk.org/materials/how-to-update-a-profile In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll. schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to create a new Bioschemas profile

In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile.

Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile

How to create a new Bioschemas profile http://tess.elixir-uk.org/materials/how-to-create-a-new-bioschemas-profile In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile. schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to check your Bioschemas deployment

This guide will show you how to check your deployed markup, both locally and what is retrieved by external services.

Keywords: schemaorg, JSON-LD, bioschemas

How to check your Bioschemas deployment http://tess.elixir-uk.org/materials/how-to-check-your-bioschemas-deployment This guide will show you how to check your deployed markup, both locally and what is retrieved by external services. schemaorg, JSON-LD, bioschemas
How to mark up your own resource with Bioschemas

In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile

Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas

How to mark up your own resource with Bioschemas http://tess.elixir-uk.org/materials/how-to-mark-up-your-own-resource-with-bioschemas In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Adding Schema.org to a GitHub Pages site

This guide will show you how to do add Schema.org markup to a GitHub Pages site.

Keywords: schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages

Adding Schema.org to a GitHub Pages site http://tess.elixir-uk.org/materials/adding-schema-org-to-a-github-pages-site-deb50140-9274-4c87-9eda-5361cb287e71 This guide will show you how to do add Schema.org markup to a GitHub Pages site. schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages
Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science http://tess.elixir-uk.org/materials/introduction-to-research-data-management-data-management-planning-and-services-provided-by-csc-it-center-for-science Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project. Maria Lehtivaara DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE Researchers Life Science Researchers Undergraduate students Master students PhD candidates postdoctoral researchers Senior Researchers, Lab Managers, Postdocs and PhD Students with basic knowledge of DMPs. Participants in the "Introduction to Data Management Plans" workshop.
Detecting differentially expressed genes with RNA-seq 11.9.2019

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and...

Scientific topics: RNA-Seq

Detecting differentially expressed genes with RNA-seq 11.9.2019 http://tess.elixir-uk.org/materials/detecting-differentially-expressed-genes-with-rna-seq This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the workshop is thus suitable for everybody. RNA-Seq
Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Single cell RNA-seq data analysis using Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
Introduction to using cloud and containers for training - OpenStack and Docker oriented view

This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object...

Keywords: Cloud computing, Containers

Resource type: Slides, course materials

Introduction to using cloud and containers for training - OpenStack and Docker oriented view http://tess.elixir-uk.org/materials/introduction-to-using-cloud-and-containers-for-training-openstack-and-docker-oriented-view This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object storage. The original material was produced by Shubham Kapoor and Johan Guldmyr, and it was tailored for trainers by Jarno Laitinen. Eija Korpelainen Cloud computing, Containers Trainers
Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

Resource type: course materials, Video

Community analysis of amplicon sequencing data (16S rRNA) http://tess.elixir-uk.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

Virus detection using small RNA-seq http://tess.elixir-uk.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

Scientific topics: RNA-Seq

Resource type: course materials, Video

RNA-seq data analysis http://tess.elixir-uk.org/materials/rna-seq-data-analysis-with-chipster This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
Metagenomics data analysis

This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...

Scientific topics: Metagenomics

Resource type: Video, course materials

Metagenomics data analysis http://tess.elixir-uk.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics