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20 materials found

Authors: Obi Griffith  or joachimwolff  or Egon Willighagen 


Groovy Cheminformatics with the Chemistry Development Kit

Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.

Scientific topics: Cheminformatics, Chemistry

Resource type: Book

Groovy Cheminformatics with the Chemistry Development Kit https://tess.elixir-europe.org/materials/groovy-cheminformatics-with-the-chemistry-development-kit Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language. Cheminformatics Chemistry PhD candidates Master students Chemists Biologists
How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data

This tutorial how to statistically analyze microarray data with ArrayAnalysis.org website.

Keywords: ArrayAnalysis.org, microarray

How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data https://tess.elixir-europe.org/materials/how-to-use-the-statistics-module-of-arrayanalysis-org-for-statistics-analysis-of-microarray-data This tutorial how to statistically analyze microarray data with ArrayAnalysis.org website. ArrayAnalysis.org, microarray post-docs
Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial

Adding nanomaterial data https://tess.elixir-europe.org/materials/adding-nanomaterial-data This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format. Database management Toxicology nanotoxicology, enanomapper, resource description framework, ontology programmers data entering
Programming in the Life Sciences

This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.

Scientific topics: Pharmacology, Drug discovery

Programming in the Life Sciences https://tess.elixir-europe.org/materials/programming-in-the-life-sciences This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API. Pharmacology Drug discovery bioinformaticians
Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2018-module-3-expression-and-differential-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows
How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping.

Scientific topics: Genetic variation, Genomics

Resource type: Tutorial

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. Genetic variation Genomics Biologists
#metawinterschool contribution by BiGCaT

Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.

Scientific topics: Metabolomics

Keywords: Metabolomics, Identifiers

Resource type: Tutorial

#metawinterschool contribution by BiGCaT https://tess.elixir-europe.org/materials/metawinterschool-contribution-by-bigcat Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis. Metabolomics Metabolomics, Identifiers Biologists
BridgeDbR Tutorial

Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites.

Resource type: Tutorial, Vignette

BridgeDbR Tutorial https://tess.elixir-europe.org/materials/bridgedbr-tutorial Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites. Biologists Chemists
Informatics for RNA-Seq Analysis 2017 Module 3-Expression and Differential Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2017-module-3-expression-and-differential-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate Students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 9-Expression and Differential Expression

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 9-Expression and Differential Expression https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-9-expression-and-differential-expression Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Post-Doctoral Fellows Researchers Biologists, Genomicists, Computer Scientists
Entering and analysing nano safety data

Tutorial that covers various aspects of working with the eNanoMapper database. It discussed searching, adding, and downloading data from an eNanoMapper database.

Keywords: ontologies, enanomapper

Entering and analysing nano safety data https://tess.elixir-europe.org/materials/entering-and-analysing-nano-safety-data Tutorial that covers various aspects of working with the eNanoMapper database. It discussed searching, adding, and downloading data from an eNanoMapper database. ontologies, enanomapper Bioinformatician PhD students post-docs
Adding ontology terms

This tutorial describes how terms can be added to the eNanoMapper ontology.

Keywords: ontologies, enanomapper

Adding ontology terms https://tess.elixir-europe.org/materials/adding-ontology-terms This tutorial describes how terms can be added to the eNanoMapper ontology. ontologies, enanomapper post-docs
Genome Annotation - Genome Annotation

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

Resource type: Tutorial

Genome Annotation - Genome Annotation https://tess.elixir-europe.org/materials/genome-annotation-genome-annotation Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé

This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online.

Keywords: nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé

Resource type: Tutorial

Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé https://tess.elixir-europe.org/materials/browsing-the-enanomapper-ontology-with-bioportal-aberowl-and-protege This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online. nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé PhD students post-docs
Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - Why is a Hi-C analysis useful? - What is...

Resource type: Tutorial

Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://tess.elixir-europe.org/materials/epigenetics-hi-c-analysis-of-drosophila-melanogaster-cells-using-hicexplorer DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - Why is a Hi-C analysis useful? - What is 'chromosome conformation capture'? - What are main steps in order to generate and plot a Hi-C contact matrix?
Introduction to Galaxy Analyses - IGV Introduction

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Tutorial

Introduction to Galaxy Analyses - IGV Introduction https://tess.elixir-europe.org/materials/galaxy-introduction-igv-introduction Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC -...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://tess.elixir-europe.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1 ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC - Perform read trimming with Trimmomatic - Align trimmed reads with BWA - Assess quality and reproducibility of experiments - Identify Tal1 binding sites with MACS2 - Determine unique/common Tal1 binding sites from G1E and Megakaryocytes - Identify unique/common Tal1 peaks occupying gene promoters - Visually inspect Tal1 peaks with Trackster
Epigenetics - DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - What is methylation and why it cannot be...

Resource type: Tutorial

Epigenetics - DNA Methylation data analysis https://tess.elixir-europe.org/materials/epigenetics-dna-methylation-data-analysis DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - What is methylation and why it cannot be recognised by a normal NGS procedure? - Can a different methylation influence the expression of a gene? How? - Which tools you can use to analyse methylation data? Objectives of the tutorial: - Learn how to analyse methylation data - Get a first intuition what are common pitfalls.
Epigenetics - Introduction to DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Epigenetics - Introduction to DNA Methylation data analysis https://tess.elixir-europe.org/materials/epigenetics-introduction DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
Sequence analysis - Mapping

Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

Resource type: Tutorial

Sequence analysis - Mapping https://tess.elixir-europe.org/materials/analysis-of-sequences-mapping Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data