Register training material
18 materials found

Authors: Aidan Budd  or Egon Willighagen 


BridgeDbR Tutorial

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

Keywords: ELIXIR RIR, BridgeDb

BridgeDbR Tutorial http://tess.elixir-uk.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902 This tutorial describes how to use the BridgeDbR package for identifier mapping. 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

OpenRiskNet: Ontology Walkthrough and Workshop http://tess.elixir-uk.org/materials/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. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Adding ontology terms

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

Keywords: enanomapper, ontologies

Resource type: Tutorial

Adding ontology terms http://tess.elixir-uk.org/materials/adding-ontology-terms-2d31ae63-7f7b-45df-aa37-4b1e14209183 This tutorial describes how terms can be added to the eNanoMapper ontology. enanomapper, ontologies post-docs
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

Groovy Cheminformatics with the Chemistry Development Kit http://tess.elixir-uk.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. Chemistry Cheminformatics 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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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
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: Genomics, Genetic variation

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene http://tess.elixir-uk.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. Genomics Genetic variation ELIXIR RIR, BridgeDb 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, ELIXIR RIR, BridgeDb

Resource type: Tutorial

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

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

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial, Vignette

BridgeDbR Tutorial http://tess.elixir-uk.org/materials/bridgedbr-tutorial Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites. ELIXIR RIR, BridgeDb Biologists Chemists
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 http://tess.elixir-uk.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: enanomapper, ontologies

Adding ontology terms http://tess.elixir-uk.org/materials/adding-ontology-terms This tutorial describes how terms can be added to the eNanoMapper ontology. enanomapper, ontologies post-docs
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 http://tess.elixir-uk.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
Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies http://tess.elixir-uk.org/materials/introduction-to-multiple-sequence-alignments-msas-and-phylogenies Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
Summarising sets of phylogenies

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics

Summarising sets of phylogenies http://tess.elixir-uk.org/materials/summarising-sets-of-phylogenies A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes examples of applications of these tools, along with introducing ideas of tree topology and some terminology associated with it. Designed for remote training. Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics Bench biologists 2013-10-23 2017-10-09
Introduction to Multiple Sequence Alignment

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

Keywords: Multiple sequence analysis, Protein structure, Sequence analysis

Introduction to Multiple Sequence Alignment http://tess.elixir-uk.org/materials/introduction-to-multiple-sequence-alignment An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of alignmetns (structural and evolutionary), and ways of building manual and automatic alignments, and an introduction to JalView Multiple sequence analysis, Protein structure, Sequence analysis Bench biologists 2013-10-23 2017-10-09
Introduction to Bioinformatics

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Keywords: Introduction bioinformatics

Introduction to Bioinformatics http://tess.elixir-uk.org/materials/introduction-to-bioinformatics An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could be wrong, and what we can do to spot it. Introduction bioinformatics Bench biologists 2013-10-23 2017-10-09
Interpreting Phylogenies

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: Molecular evolution, Phylogenetics

Interpreting Phylogenies http://tess.elixir-uk.org/materials/interpreting-phylogenies Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic trees. Includes exercises on visulaising and manipulating trees using Dendroscope and NJplot to reinforce some of these ideas, while also providing a very basic overview of steps involved in a generic phylogenetic analysis. Molecular evolution, Phylogenetics experimeintal biologist researchers field biologist researchers 2013-09-13 2017-10-09