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18 materials found

Authors: erasche  or Egon Willighagen 


BridgeDbR Tutorial

This tutorial describes how to use the BridgeDbR package for identifier mapping.

Keywords: ELIXIR RIR, BridgeDb

OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

Adding ontology terms

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

Keywords: enanomapper, ontologies

Resource type: Tutorial

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: Chemistry, Cheminformatics

Resource type: Book

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

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

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

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. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.

Scientific topics: Genomics, Genetic variation

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

#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, ELIXIR RIR, BridgeDb

Resource type: Tutorial

BridgeDbR Tutorial

BridgeDb is a combination of an application programming interface (API), library, and set of data files for mapping identifiers for identical objects [1]. Identifier mapping databases are available for gene products and metabolites. This Bioconductor Vignette explains how to use BridgeDb in the R...

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial, Vignette

Galaxy Server administration - Ansible

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • Why Ansible?
  • How and when to use Ansible?
  • How to write a role?
  • How to leverage community build roles?

Objectives of the tutorial:

  • Learn Ansible basics
  • Write a simple role
  • Install a...

Resource type: Tutorial

Data Manipulation - Collections: Rule Based Uploader

A collection of microtutorials explaining data manipulation within Galaxy

Questions of the tutorial:

  • How to use the rule based uploader to create complex collections

Objectives of the tutorial:

  • Learn about the Rule Based Uploader

Resource type: Tutorial

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

Adding ontology terms

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

Keywords: enanomapper, ontologies

Contributing to the Galaxy Training Material - Creating a new tutorial - Slides

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Slides

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

Development in Galaxy - Galaxy Interactive Environments

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Interactive Environments (GIEs)?
  • How to enable GIEs in Galaxy?
  • How to develop your own...

Resource type: Slides

Galaxy Server administration - Advanced customisation of a Galaxy instance

Resources related to configuration and maintenance of Galaxy servers

Resource type: Slides