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Related resources: Proteomics dataset  or Contributing to the Galaxy ... 


Contributing to the Galaxy Training Material - Contributing with GitHub via command-line

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: Tutorial

Contributing to the Galaxy Training Material - Contributing with GitHub via command-line http://tess.elixir-uk.org/materials/contributing-to-the-galaxy-training-material-contributing-with-github-via-command-line 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 accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy. Questions of the tutorial: - How can I contribute to an open-source project with GitHub? - What is the GitHub flow? Objectives of the tutorial: - Fork a repository on GitHub - Clone a remote repository locally - Create a branch - Commit changes - Push changes to a remote repository - Create a pull request - Update a pull request
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.
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.
Proteomics - Metaproteomics tutorial

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data? - How can I perform taxonomy analysis and visualize metaproteomics data? - How can I perform...

Resource type: Tutorial

Proteomics - Metaproteomics tutorial http://tess.elixir-uk.org/materials/proteomics-metaproteomics-tutorial Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data? - How can I perform taxonomy analysis and visualize metaproteomics data? - How can I perform functional analysis on this metaproteomics data? Objectives of the tutorial: - A taxonomy and functional analysis of metaproteomic mass spectrometry data.