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15 materials found

Authors: Jan Slifka  or nekrut 


DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides

Data Manipulation - Collections: Multisample Analysis

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Tutorial

Data Manipulation - Collections: Using dataset collection

A collection of microtutorials explaining data manipulation within Galaxy

Questions of the tutorial:

  • How to manipulate large numbers of datasets at once?

Objectives of the tutorial:

  • Understand and master dataset collections

Resource type: Tutorial

User Interface and Features - Histories: Understanding Galaxy history system

A collection of microtutorials explaining various features of the Galaxy user interface

Questions of the tutorial:

  • How do Galaxy histories work?

Objectives of the tutorial:

  • Gain understanding on navigating and manipulating histories

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome

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

Variant Analysis - Calling very rare variants

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • What frequency of variants is so low that it is obscured by sequencing error rate?
  • What are the different types of consensus sequences produced from duplex sequencing?

Objectives of...

Resource type: Tutorial

Variant Analysis - Calling variants in diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How to find variable sites in diploid genomes?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in human genome.

Resource type: Tutorial

Variant Analysis - Calling variants in non-diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How does frequency of mitochondrial polymorphisms change from mother to child?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in bacteria,...

Resource type: Tutorial

Introduction to Galaxy Analyses - NGS data logistics

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 manipulate and process...

Resource type: Tutorial

Transcriptomics - Reference-based RNAseq data analysis (long)

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How to perform analysis of RNAseq data when reference genome is available?

Objectives of the tutorial:

  • Learns basic concepts of RNAseq analysis

Resource type: Tutorial

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

Introduction to Galaxy Analyses - IGV Introduction

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.

Resource type: Tutorial

Introduction to Galaxy Analyses - Galaxy 101

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:

  • Which coding exon has the...

Resource type: Tutorial