Register training material
1501 materials found

06: Gene Set Enrichment -- Introduction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

06: Gene Set Enrichment -- Introduction https://tess.elixir-europe.org/materials/06-gene-set-enrichment-introduction Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Intro
05: Bioconductor Annotation Resources

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

05: Bioconductor Annotation Resources https://tess.elixir-europe.org/materials/05-bioconductor-annotation-resources Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Intro
04: Practical: Organizing data with SummarizedExperiment

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

04: Practical: Organizing data with SummarizedExperiment https://tess.elixir-europe.org/materials/04-practical-organizing-data-with-summarizedexperiment Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Intro
03: Core approaches in Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

03: Core approaches in Bioconductor https://tess.elixir-europe.org/materials/03-core-approaches-in-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Intro
02: Practical: R / Bioconductor and Reproducible Research

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

02: Practical: R / Bioconductor and Reproducible Research https://tess.elixir-europe.org/materials/02-practical-r-bioconductor-and-reproducible-research Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Intro
01: Introduction to R and Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

01: Introduction to R and Bioconductor https://tess.elixir-europe.org/materials/01-introduction-to-r-and-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Intro
Training on integration of OpenID Connect services to ELIXIR AAI

Materials for hands-on training on connection OpenID Connect relaying party to ELIXIR AAI.

Keywords: AAI, OpenID Connect, Authentication

Training on integration of OpenID Connect services to ELIXIR AAI https://tess.elixir-europe.org/materials/training-on-integration-of-openid-connect-services-to-elixir-aai Materials for hands-on training on connection OpenID Connect relaying party to ELIXIR AAI. AAI, OpenID Connect, Authentication service administrators in organizations that want to make use of ELIXIR AAI
Regular expressions

This course introduces regular expressions and how to search for text patterns in a number of programming languages (UNIX command line, R, Python etc.). It is aimed at colleagues who are going to run analysis programs on their own or wish to use computing clusters.

Regular expressions https://tess.elixir-europe.org/materials/regular-expressions This course introduces regular expressions and how to search for text patterns in a number of programming languages (UNIX command line, R, Python etc.). It is aimed at colleagues who are going to run analysis programs on their own or wish to use computing clusters.
AWK and BASH scripting

This course introduces scripting with AWK and BASH. It is aimed at colleagues who are going to run analysis programs on their own or wish to use computing clusters.

AWK and BASH scripting https://tess.elixir-europe.org/materials/awk-and-bash-scripting This course introduces scripting with AWK and BASH. It is aimed at colleagues who are going to run analysis programs on their own or wish to use computing clusters.
Bioinformatics - the Power of Computers in Biology: A Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in...

Scientific topics: Sequence analysis

Keywords: Basic bioinformatics, Basic linux commands, Bioinformatics schools, Gene loss, Genetic mutation, Raspberry pi computers, Sequence analysis, Sequence database searching, Training materials

Bioinformatics - the Power of Computers in Biology: A Practical Guide https://tess.elixir-europe.org/materials/bioinformatics-the-power-of-computers-in-biology-a-practical-guide This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in humans. Analyses are run both online and at the command line, the latter using Raspberry Pi computers running the 4273π variant of Linux (4273pi.org). Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how similar functionality can be achieved using the Linux command line. On reading the Guide and completing the exercises, users will be able to: i) search biological sequence databases using the online program BLAST, and navigate GenPept sequence records; ii) execute some basic Linux commands to perform a set of simple file-manipulation tasks; iii) perform BLAST searches via the Linux command line; and iv) evaluate the biological implications of search results, with reference to mutations and function. Sequence analysis Basic bioinformatics, Basic linux commands, Bioinformatics schools, Gene loss, Genetic mutation, Raspberry pi computers, Sequence analysis, Sequence database searching, Training materials 2019-06-08
A Critical Guide to the neXtProt knowledgebase: querying using SPARQL

This Critical Guide in the Introduction to Bioinformatics series briefly outlines how to explore the neXtProt human protein database using SPARQL. While text indexation has made database contents more accessible, being able to combine search criteria for specific content permits more powerful...

Scientific topics: Database management

Keywords: Human protein database, Introduction bioinformatics, Introduction nextprot, Nextprot data model, Rdf triples, Semantic triples, Sparql queries, Sparql syntax, Training material

A Critical Guide to the neXtProt knowledgebase: querying using SPARQL https://tess.elixir-europe.org/materials/a-critical-guide-to-the-nextprot-knowledgebase-querying-using-sparql This Critical Guide in the Introduction to Bioinformatics series briefly outlines how to explore the neXtProt human protein database using SPARQL. While text indexation has made database contents more accessible, being able to combine search criteria for specific content permits more powerful querying, and provides a means to mine the information stored in databases. This Guide illustrates the use of the SPARQL semantic query language to interrogate neXtProt and other databases that provide SPARQL endpoints. Specifically, the Guide introduces the concept of database ‘semantic triples’, and examines features of the neXtProt data model. On reading this Guide, and completing the exercises, users will be able to: i) identify key entities within the neXtProt data model; ii) explain what these entities represent, what information they contain and what the information is used for; iii) identify key SPARQL syntax elements; iv) understand SPARQL tutorial examples; and v) write a SPARQL query to retrieve entries matching specific criteria. Database management Human protein database, Introduction bioinformatics, Introduction nextprot, Nextprot data model, Rdf triples, Semantic triples, Sparql queries, Sparql syntax, Training material Beginners 2019-06-06
Essential Steps of the FAIRification Process

Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops". This material documents the accumulated practical & teaching...

Keywords: FAIR, data stewardship, metadata, linked data

Resource type: Training materials

Essential Steps of the FAIRification Process https://tess.elixir-europe.org/materials/essential-steps-of-the-fairification-process Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops". This material documents the accumulated practical & teaching experiences from BYODS as well as more high-level FAIR awareness trainings. This document was formerly known as the "Big Book of FAIRification". FAIR, data stewardship, metadata, linked data Researchers Support Staff data librarians software developers, bioinformaticians
FAIR Data Stewardship - Data sharing, archiving and publishing

The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities...

Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

Resource type: Slides, Training materials

FAIR Data Stewardship - Data sharing, archiving and publishing https://tess.elixir-europe.org/materials/fair-data-stewardship-data-sharing-archiving-and-publishing The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities towards data are distributed. The course does not require any prior knowledge. Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication General Interest Scientists Researchers data stewards
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 https://tess.elixir-europe.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
Developing robust and efficient code

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Developing robust and efficient code https://tess.elixir-europe.org/materials/developing-robust-and-efficient-code Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Workshop
102: Solving common bioinformatic challenges using GenomicRanges

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

102: Solving common bioinformatic challenges using GenomicRanges https://tess.elixir-europe.org/materials/102-solving-common-bioinformatic-challenges-using-genomicranges Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Genomics
250: Working with genomic data in R with the DECIPHER package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Genomic data

250: Working with genomic data in R with the DECIPHER package https://tess.elixir-europe.org/materials/250-working-with-genomic-data-in-r-with-the-decipher-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Genomic data
500: Effectively using the DelayedArray framework to support the analysis of large datasets

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Large data

500: Effectively using the DelayedArray framework to support the analysis of large datasets https://tess.elixir-europe.org/materials/500-effectively-using-the-delayedarray-framework-to-support-the-analysis-of-large-datasets Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Large data
510: Maintaining your Bioconductor package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Packages

510: Maintaining your Bioconductor package https://tess.elixir-europe.org/materials/510-maintaining-your-bioconductor-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Packages
R / Bioconductor for open-source analysis and comprehension of high-throughput genomic data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

R / Bioconductor for open-source analysis and comprehension of high-throughput genomic data https://tess.elixir-europe.org/materials/r-bioconductor-for-open-source-analysis-and-comprehension-of-high-throughput-genomic-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Open Targets: Using Genetics and Functional Genomics to Identify and Prioritise Targets for New Medicines

Materials of the ASHG Workshop 2018, that will guide you through the detailed functionality of Open Targets' new User Interface for Statistical Geneticists - Open Targets Genetics.

Keywords: Open Targets Genetics

Open Targets: Using Genetics and Functional Genomics to Identify and Prioritise Targets for New Medicines https://tess.elixir-europe.org/materials/open-targets-using-genetics-and-functional-genomics-to-identify-and-prioritise-targets-for-new-medicines Materials of the ASHG Workshop 2018, that will guide you through the detailed functionality of Open Targets' new User Interface for Statistical Geneticists - Open Targets Genetics. Open Targets Genetics
PanelApp Reviewer’s Guide

This presentation provides a guide to how to make reviews of gene-disease evidence in the PanelApp database.

Scientific topics: Rare diseases, Genomics

Keywords: Gene lists, Genomics, human disease, Biocuration

Resource type: knowledgebase

PanelApp Reviewer’s Guide https://tess.elixir-europe.org/materials/panelapp-reviewer-s-guide This presentation provides a guide to how to make reviews of gene-disease evidence in the PanelApp database. Rare diseases Genomics Gene lists, Genomics, human disease, Biocuration Clinical Scientists clinicians and informaticians interested in cancer genetics Researchers
BioC 2018: Where Software and Biology Connect

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Conference

BioC 2018: Where Software and Biology Connect https://tess.elixir-europe.org/materials/bioc-2018-where-software-and-biology-connect Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Conference
HCABrowser for discovery and access

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCABrowser for discovery and access https://tess.elixir-europe.org/materials/hcabrowser-for-discovery-and-access Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
HCAMatrixBrowser for retrieving count matrices

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCAMatrixBrowser for retrieving count matrices https://tess.elixir-europe.org/materials/hcamatrixbrowser-for-retrieving-count-matrices Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Getting started with Bioschemas

### "How to do" guidelines about: * What and why schema.org * What and why bioschemas.org * How-to select the right profile for your resource * How-to mark up your own resource with Bioschemas

Keywords: Bioschemas, Standards

Getting started with Bioschemas https://tess.elixir-europe.org/materials/getting-started-with-bioschemas ### "How to do" guidelines about: * What and why schema.org * What and why bioschemas.org * How-to select the right profile for your resource * How-to mark up your own resource with Bioschemas Bioschemas, Standards
CWL User Guide

This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0.

Keywords: CWL, commonwl, Workflows

Resource type: Tutorial

CWL User Guide https://tess.elixir-europe.org/materials/cwl-user-guide This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0. CWL, commonwl, Workflows bioinformaticians tool authors
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Biology, Bioinformatics, Computer science

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Biology Bioinformatics Computer science High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
NanoCommons - Data Management in Nano Safety Research

Nanosafety research is rapidly transforming into a highly competitive and data-intensive field. Translational research, the introduction of nanoinformatics and the shift towards big data introduce the need for complex data capture, storage, handling, and analysis. This combination is called data...

Scientific topics: Data management

Resource type: Video

NanoCommons - Data Management in Nano Safety Research https://tess.elixir-europe.org/materials/nanocommons-data-management-in-nano-safety-research Nanosafety research is rapidly transforming into a highly competitive and data-intensive field. Translational research, the introduction of nanoinformatics and the shift towards big data introduce the need for complex data capture, storage, handling, and analysis. This combination is called data management and is the most neglected aspect of scientific research. Data management
bio.tools & EDAM drop-in hackathon & discussions

bio.tools, EDAM drop-in hackathon and discussions

Keywords: biohackaton 2018

bio.tools & EDAM drop-in hackathon & discussions https://tess.elixir-europe.org/materials/bio-tools-edam-drop-in-hackathon-discussions bio.tools, EDAM drop-in hackathon and discussions biohackaton 2018