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
Introduction to Protein Structure Analysis
This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure....
Operations: Visualisation
Keywords: Protein structure visualisation
Resource type: e-learning
Introduction to Protein Structure Analysis
https://elearning.bits.vib.be/courses/protein-structure-analysis/
http://tess.elixir-uk.org/materials/introduction-to-protein-structure-analysis
This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins (without any structure information) and to find homologous structures. We will use online tools to quantify various interactions in the structures.
## Objectives
* Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it.
* Display protein structure data and compare structures, through the use of Yasara.
* Create high-quality graphical representations of the structures.
* Calculate the effect of mutations on the stability of your protein.
Alexander Botzki
Joost Van Durme
Janick Mathys
Protein structure visualisation
Life Science Researchers
Preserve, publish and share your data
- why preserve data
- what data should be preserved
- how share data
- where to deposit your data
- Fairsharing, re3data
- ELIXIR Core Resources
- Data Formats
- Generic archives
Scientific topics: Data management, Data submission, annotation, and curation
Keywords: data formats, ELIXIR Core resources, FAIR data submission
Resource type: Presentation
Preserve, publish and share your data
https://osf.io/whj7t/
http://tess.elixir-uk.org/materials/preserve-publish-and-share-your-data
- why preserve data
- what data should be preserved
- how share data
- where to deposit your data
- Fairsharing, re3data
- ELIXIR Core Resources
- Data Formats
- Generic archives
Alexander Botzki
Data management
Data submission, annotation, and curation
data formats, ELIXIR Core resources, FAIR data submission
life scientists
Reusing existing data
- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub)
- licenses
- datasets as first-class research products
- research software as first-class research products
- data citations
Scientific topics: Data management
Keywords: data licenses, software licenses, data journal
Resource type: Presentation
Reusing existing data
https://osf.io/syx4m/
http://tess.elixir-uk.org/materials/reusing-existing-data
- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub)
- licenses
- datasets as first-class research products
- research software as first-class research products
- data citations
Alexander Botzki
Data management
data licenses, software licenses, data journal
life scientists
Research Data Management in Life Sciences
The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.
Scientific topics: Data management
Resource type: Presentation, Vignette, Video
Research Data Management in Life Sciences
https://osf.io/fpvgy/
http://tess.elixir-uk.org/materials/research-data-management-in-life-sciences
The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.
Alexander Botzki
Laura Standaert
Tuur Muyldermans
Hanne Elsen
Paula Oset
Thomas Van de Velde
Flora D'Anna
Nele Pauwels
Griet Den Herder
Jan Lammertyn
Data management
Life Science Researchers
Data Management and Writing a Data Management Plan
Writing a Data Management Plan
A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data.
Scientific topics: Data management
Resource type: e-learning
Data Management and Writing a Data Management Plan
https://elearning.bits.vib.be/courses/writing-a-data-management-plan/
http://tess.elixir-uk.org/materials/data-management-and-writing-a-data-management-plan
Writing a Data Management Plan
A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data.
Alexander Botzki
Geert Bonamie
Data management
