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Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle

This material is part of an follow up FAIR data stewardship workshop for the Marie Curie ITN ProEVLifeCycle (The prostate cancer Extracellular Vesicle LifeCycle)

FAIR and data stewardship - November 3th, 2021
Organiser: Dutch Techcentre For Life Sciences, DTL
Setup: Virtual meeting...

Scientific topics: FAIR data, Data management

Operations: Analysis, Data handling

Keywords: Data analysis, Data management planning, Data processing, Data sharing, Data collection, Data preserving, Data reuse

Resource type: Slidedeck

Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Transcriptomics - Visualization of RNA-Seq results with CummeRbund

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How are RNA-Seq results stored?
  • Why are visualization techniques needed?
  • How to select our desired subjects for differential gene expression analysis?

Objectives of the tutorial:

  • Manage RNA-Seq...

Resource type: Tutorial

Development in Galaxy - Visualizations: generic plugins

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can visualization plugins benefit science?

Objectives of the tutorial:

  • Implement a first Galaxy...

Resource type: Tutorial

Development in Galaxy - Galaxy Webhooks

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Webhooks?
  • How to create them?

Objectives of the tutorial:

  • Discover what Galaxy...

Resource type: Tutorial

Development in Galaxy - Visualizations: charts plugins

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • How can I make a custom plugin for Charts?

Objectives of the tutorial:

  • Learn how to add custom...

Resource type: Tutorial

Assembly - De Bruijn Graph Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Introduction to Genome Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Sequence analysis - Mapping

Analyses of sequences

Questions of the tutorial:

  • What two things are crucial for a correct mapping?
  • What is BAM?

Objectives of the tutorial:

  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data

Resource type: Tutorial

Sequence analysis - Quality Control

Analyses of sequences

Questions of the tutorial:

  • How to control quality of NGS data?
  • What are the quality parameters to check for each dataset?
  • How to improve the quality of a sequence dataset?

Objectives of the tutorial:

  • Manipulate FastQ files
  • Control quality from a FastQ file -...

Resource type: Tutorial