Containers & Workflow pipelines workshop
The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...
Keywords: Containers, Nextflow
Resource type: Training materials
Containers & Workflow pipelines workshop
https://nextflow-workshop.readthedocs.io/en/latest/
http://tess.elixir-uk.org/materials/containers-workflow-pipelines-workshop
The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, at the end of the first day, Singularity will be highlighted as well.
On the second day (27 May 2021), you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language.
Alexander Botzki
Tuur Muyldermans
Containers, Nextflow
bioinformaticians
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 ID using OpenMS tools
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-oms/tutorial.html
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.
stortebecker
bgruening
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...
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-quant-sil/tutorial.html
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.
stortebecker
bgruening
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.
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html
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.
stortebecker
bgruening
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...
Proteomics - Secretome Prediction
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/secretome-prediction/tutorial.html
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.
stortebecker
bgruening
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...
Proteomics - Metaproteomics tutorial
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html
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.
timothygriffin
pratikdjagtap
jj-umn
blankclemens
