Difference between revisions of "Tutorials"

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These are tutorials created by [[European Proteomics Academy:People|us]] (or our collaborators) especially for this page:
 
These are tutorials created by [[European Proteomics Academy:People|us]] (or our collaborators) especially for this page:
  
* Introducing [[Tutorials:Search Engines|Search engines]] (example of a search engine page is the [[MSAmanda]] page)
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* Introducing [[Tutorials:Search Engines|search engines]] (example of a search engine page is the [[MSAmanda]] page)
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* Introducing [[Tutorials:Distributed Computing|distributed computing]] (example of a distributed computing page is the [[Pladipus]] page)
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== External Tutorials ==
 
== External Tutorials ==
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=== MaxQuant/Perseus Tutorials ===
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The documentation of [[MaxQuant]] and [[Perseus]] contains abundant teaching material on the interpretation of quantitative data and associated statistics.
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The documentation of both tools can be found [http://www.coxdocs.org here].
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=== Skyline Tutorials ===
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The [[Skyline]] wiki provides several tutorials on how to use the software.
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The complete list can be found [https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials here].
  
 
=== Compomics Tutorials ===
 
=== Compomics Tutorials ===
The [https://compomics.com Computational Omics and Systems Biology] Group at the VIB-UGent provide excellent tutorials using their rich set of user-friendly proteomics bioinformatics tools, most importantly [[SearchGUI]] and [[PeptideShaker]].
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The [https://compomics.com Computational Omics and Systems Biology] Group at the VIB-UGent provide tutorials using user-friendly proteomics bioinformatics tools, most importantly [[SearchGUI]] and [[PeptideShaker]].
  
 
The complete list of tutorials can be found at https://compomics.com/bioinformatics-for-proteomics/.
 
The complete list of tutorials can be found at https://compomics.com/bioinformatics-for-proteomics/.
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# [https://compomics.com/bioinformatics-for-proteomics/functional-analysis/ Functional analysis]
 
# [https://compomics.com/bioinformatics-for-proteomics/functional-analysis/ Functional analysis]
 
# [https://compomics.com/bioinformatics-for-proteomics/data-sharing/ Data sharing]
 
# [https://compomics.com/bioinformatics-for-proteomics/data-sharing/ Data sharing]
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=== Biocontainers ===
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The [[Biocontainers]] website contains extensive tutorials on how to design containers for bioinformatic tools.
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The documentation can be found [http://biocontainers.pro/docs/ here].
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=== Galaxy ===
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[[Galaxy-P]] has tutorials on how to run proteomics tools in [[wikipedia:Galaxy_(computational_biology)|Galaxy]].
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The tutorials can be found [https://github.com/Stortebecker/training-material/tree/master/Proteomics here].
  
 
== Online Video Tutorials ==
 
== Online Video Tutorials ==
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! Title !!Category !!Description
 
! Title !!Category !!Description
 
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|[[Tutorial:Pladipus|Pladipus]] || Intermediate / Advanced || Video tutorial on how to set a distributed computing system using [https://compomics.github.io/projects/pladipus.html Pladipus] by Kenneth Verheggen.
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|[[Video-Tutorial:Pladipus|Pladipus]] || Intermediate / Advanced || Video tutorial on how to set a distributed computing system using [https://compomics.github.io/projects/pladipus.html Pladipus] by Kenneth Verheggen.
 
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|-
 
|[https://vimeo.com/97952461 Cross Linking] || Intermediate / Advanced || Video tutorial on how to idenify cross linked peptides using [http://prospector.ucsf.edu/prospector/mshome.htm ProteinProspector] by Robert Chalkley.
 
|[https://vimeo.com/97952461 Cross Linking] || Intermediate / Advanced || Video tutorial on how to idenify cross linked peptides using [http://prospector.ucsf.edu/prospector/mshome.htm ProteinProspector] by Robert Chalkley.
 
|}
 
|}

Latest revision as of 15:48, 13 February 2017

Here we try to present a list of useful tutorials that present the basic principles of proteomics technologies.

Internal Tutorials

These are tutorials created by us (or our collaborators) especially for this page:


External Tutorials

MaxQuant/Perseus Tutorials

The documentation of MaxQuant and Perseus contains abundant teaching material on the interpretation of quantitative data and associated statistics.

The documentation of both tools can be found here.

Skyline Tutorials

The Skyline wiki provides several tutorials on how to use the software.

The complete list can be found here.

Compomics Tutorials

The Computational Omics and Systems Biology Group at the VIB-UGent provide tutorials using user-friendly proteomics bioinformatics tools, most importantly SearchGUI and PeptideShaker.

The complete list of tutorials can be found at https://compomics.com/bioinformatics-for-proteomics/.

Currently, they offer three tutorials:

  1. Identification techniques
  2. Functional analysis
  3. Data sharing

Biocontainers

The Biocontainers website contains extensive tutorials on how to design containers for bioinformatic tools.

The documentation can be found here.

Galaxy

Galaxy-P has tutorials on how to run proteomics tools in Galaxy.

The tutorials can be found here.

Online Video Tutorials

Title Category Description
Pladipus Intermediate / Advanced Video tutorial on how to set a distributed computing system using Pladipus by Kenneth Verheggen.
Cross Linking Intermediate / Advanced Video tutorial on how to idenify cross linked peptides using ProteinProspector by Robert Chalkley.