1. Home
  2. Materials
Register training material
18 materials found

Node: Finland 

Tutorial on working with computing clusters

This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system.

Keywords: HPC

Resource type: Tutorial

Tutorial on working with computing clusters http://tess.elixir-uk.org/materials/tutorial-on-working-with-computing-clusters This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system. HPC Novice users of HPC and anyone who expects to need to use HPC systems at some stage in their research
Tutorial on using MPI with containers

In this material we will briefly touch upon why MPI is such a tricky component, explain the main approaches to combine MPI with containers and discuss when it is actually worthwhile to use MPI containers.

Keywords: MPI, Containers, Computer Programming, Documentation and help

Resource type: Tutorial

Tutorial on using MPI with containers http://tess.elixir-uk.org/materials/tutorial-on-using-mpi-with-containers In this material we will briefly touch upon why MPI is such a tricky component, explain the main approaches to combine MPI with containers and discuss when it is actually worthwhile to use MPI containers. MPI, Containers, Computer Programming, Documentation and help Users wanting to construct MPI containers Developers wanting to distribute their MPI dependent software HPC system maintainers wanting to enable MPI containers
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.
GA4GH Passports and ELIXIR AAI

The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API.

Keywords: AAI , GA4GH, Passports, Auhtorisation

Resource type: Training materials, Video

GA4GH Passports and ELIXIR AAI http://tess.elixir-uk.org/materials/ga4gh-passports-and-elixir-aai The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API. Stefan Negru Teemu Kataja AAI , GA4GH, Passports, Auhtorisation software developers, bioinformaticians
Integrating to ELIXIR AAI -- instructions for developers

This is a collection of videos, presentations and on-line materials for developers and administrators for integrating a service to ELIXIR AAI, the ELIXIR Compute platform service for user authentication and authorisation.

Scientific topics: Computer science

Keywords: AAI, IAM, Authentication, authorisation

Resource type: Webinar, Presentation, Documentation

Integrating to ELIXIR AAI -- instructions for developers http://tess.elixir-uk.org/materials/integrating-to-elixir-aai-instruction-for-developers This is a collection of videos, presentations and on-line materials for developers and administrators for integrating a service to ELIXIR AAI, the ELIXIR Compute platform service for user authentication and authorisation. Computer science AAI, IAM, Authentication, authorisation software developers, bioinformaticians
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](https://www.csc.fi/en/web/training/-/pouta-cloud-course-2018) which consists of lectures and hands-on [exercises](https://chipster.csc.fi/material/cloud/exercises.pdf) on creating and managing virtual resources in OpenStack (VM, volumes,...

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](https://www.csc.fi/en/web/training/-/pouta-cloud-course-2018) which consists of lectures and hands-on [exercises](https://chipster.csc.fi/material/cloud/exercises.pdf) 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
How to install and deploy Beacon

**This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.**

Scientific topics: Genomics

Keywords: genomics, open access, eLearning, EeLP

Resource type: Video, Manual, Slides, Installation instructions

How to install and deploy Beacon http://tess.elixir-uk.org/materials/how-to-install-and-deploy-beacon **This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.** Juha Tornroos Sabela de la Torre Jordi Rambla Genomics genomics, open access, eLearning, EeLP life scientists Researchers
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions http://tess.elixir-uk.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Transcriptomics, Genomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

RNA-seq data analysis using Chipster http://tess.elixir-uk.org/materials/rna-seq-data-analysis-using-chipster Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017 Eija Korpelainen Maria Lehtivaara Transcriptomics Genomics transcriptomics, RNA-Seq, eLearning, EeLP Researchers
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
Training on integration of services to ELIXIR AAI

The hands on training material is on integrating a SAML (Shibboleth) or OpenID Connect service to ELIXIR AAI, the ELIXIR service portfolio for authenticating researchers and managing their access rights to ELIXIR services.

Keywords: AAI, authentication, Shibboleth

Training on integration of services to ELIXIR AAI http://tess.elixir-uk.org/materials/training-on-integration-of-services-to-elixir-aai The hands on training material is on integrating a SAML (Shibboleth) or OpenID Connect service to ELIXIR AAI, the ELIXIR service portfolio for authenticating researchers and managing their access rights to ELIXIR services. AAI, authentication, Shibboleth service administrators in organizations that want to make use of ELIXIR AAI