Register training material
7 materials found

Authors: bgruening 

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Related resources: Input datasets 


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 http://tess.elixir-uk.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.
Proteomics - Peptide and Protein ID using OpenMS tools

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Peptide and Protein ID using OpenMS tools http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id-using-openms-tools Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.
Variant Analysis - Exome sequencing data analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to identify the genetic variation with the use of exome sequencing? - What is the pipeline of the process of finding genetic variation which caused the disease? Objectives of the...

Resource type: Tutorial

Variant Analysis - Exome sequencing data analysis http://tess.elixir-uk.org/materials/variant-analysis-exome-sequencing-data-analysis Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to identify the genetic variation with the use of exome sequencing? - What is the pipeline of the process of finding genetic variation which caused the disease? Objectives of the tutorial: - Identification of the genetic variation using the exome sequencing - Using FreeBayes calls for variants generating - Variant analysis and GEMINI queries
Introduction to Galaxy Analyses - From peaks to genes

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. Questions of the tutorial: - How to use Galaxy? - How to get...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes http://tess.elixir-uk.org/materials/galaxy-introduction-from-peaks-to-genes 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. Questions of the tutorial: - How to use Galaxy? - How to get from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are MS1 features? - How to quantify based on MS1 features? - How to map MS1 features to MS2 identifications? - How to evaluate and optimize the results? Objectives of the tutorial: - MS1 feature...

Resource type: Tutorial

Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL) http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-quantification-via-stable-isotope-labelling-sil Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are MS1 features? - How to quantify based on MS1 features? - How to map MS1 features to MS2 identifications? - How to evaluate and optimize the results? Objectives of the tutorial: - MS1 feature quantitation and mapping of quantitations to peptide and protein IDs.
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.
Proteomics - Secretome Prediction

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to predict cellular protein localization based upon GO-terms? - How to combine multiple localization predictions? Objectives of the tutorial: - Predict proteins in the cellular secretome by using...

Resource type: Tutorial

Proteomics - Secretome Prediction http://tess.elixir-uk.org/materials/proteomics-secretome-prediction Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to predict cellular protein localization based upon GO-terms? - How to combine multiple localization predictions? Objectives of the tutorial: - Predict proteins in the cellular secretome by using GO-terms. - Predict proteins in the cellular secretome by using WolfPSORT. - Combine the results of both predictions.