ELIXIR CZ Friday Coffee #5: Data Management with Data Stewardship Wizard
This short presentation was presented as part of the Friday Coffee presentation series organized by the ELIXIR CZ infrastructure and offered students a basic insight into data management and data management plans, which are important (not only) for the success of scientific projects, but...
Scientific topics: Data management
Keywords: data management plan, data stewardship, FAIR, data management, software tools
Resource type: Video, Webinar
ELIXIR CZ Friday Coffee #5: Data Management with Data Stewardship Wizard
https://youtu.be/2YGrVGa9JYY
http://tess.elixir-uk.org/materials/elixir-cz-friday-coffee-5-data-management-with-data-stewardship-wizard
This short presentation was presented as part of the Friday Coffee presentation series organized by the ELIXIR CZ infrastructure and offered students a basic insight into data management and data management plans, which are important (not only) for the success of scientific projects, but increasingly for grant applications as well. The presentation also introduced students to the possibility of creating these plans using the [Data Stewardship Wizard](https://ds-wizard.org), a tool that creates the data management plan by filling out a simple, synoptic questionnaire. It offers a simple and very effective solution without the need for deep knowledge of data stewardship or data management.
Video available [here](https://www.youtube.com/watch?v=2YGrVGa9JYY).
Jana Freeman
Tereza Machacova
Data management
data management plan, data stewardship, FAIR, data management, software tools
Researchers
data managers
data stewards
A Gentle Introduction to DSW for Convergers
[Data Stewardship Wizard](https://ds-wizard.org) 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 governance, Data management
Keywords: Data managment plan, data stewardship, data management, software tools
Resource type: Video, Slides, Webinar
A Gentle Introduction to DSW for Convergers
http://doi.org/10.5281/zenodo.4452655
http://tess.elixir-uk.org/materials/a-gentle-introduction-to-dsw-for-convergers
[Data Stewardship Wizard](https://ds-wizard.org) 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 questionnaires filled by researchers. They can then export their answers to human-readable documents following the well-known templates such as Science Europe or Horizon 2020; or machine-actionable files for further processing.
Jan Slifka
Data governance
Data management
Data managment plan, data stewardship, data management, software tools
data managers
Researchers
data stewards
DSW Template Development Kit: The Tutorial
[Data Stewardship Wizard](ds-wizard.org) is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines...
Scientific topics: Data management
Keywords: data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development
Resource type: Video, Slides, Webinar
DSW Template Development Kit: The Tutorial
http://doi.org/10.5281/zenodo.4286272
http://tess.elixir-uk.org/materials/dsw-template-development-kit-the-tutorial
[Data Stewardship Wizard](ds-wizard.org) is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines (e.g. RDF, YAML, or JSON). Our Template Development Kit (DSW TDK) is a command-line tool to make the work on templates efficient.
Marek Suchanek
Data management
data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development
data stewards
data managers
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...
Assembly - Making sense of a newly assembled genome
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.html
http://tess.elixir-uk.org/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?
Objectives of the tutorial:
- Identification of the most closely related genome to my new assembly
- Perform sequence comparison to locate rearrangements
- Identify genes located in deletions
nekrut
delphine-l
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...
Assembly - Unicycler Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html
http://tess.elixir-uk.org/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I have short reads and long reads. How do I assemble a genome?
Objectives of the tutorial:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with Prokka
nekrut
delphine-l
slugger70
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...
Assembly - De Bruijn Graph Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html
http://tess.elixir-uk.org/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- What are the factors that affect genome assembly?
- How does Genome assembly work?
Objectives of the tutorial:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an assembly using the SPAdes assembler.
slugger70
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...
Assembly - Introduction to Genome Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/general-introduction/tutorial.html
http://tess.elixir-uk.org/materials/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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- How do we perform a very basic genome assembly from short read data?
Objectives of the tutorial:
- assemble some paired end reads using Velvet
- examine the output of the assembly.
slugger70
