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Workshops and courses
Introduction to Git & GitHub
5 - 6 February 2024
Brussel, Belgium
Face-to-face
hands-on research data management basic bioinformatics ELIXIR -
Workshops and courses
Introduction to Git & GitHub
16 - 17 May 2024
Zwijnaarde, Belgium
Face-to-face
hands-on research data management basic bioinformatics ELIXIR
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Training materials
Introduction to GitHub
• beginnerGitHub Reproducibility -
Recorded webinar
PDBe tools in GitHub
Software engineering
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course materials
Introduction to GitHub for chemists
• beginnerGit GitHub -
hands-on tutorial
Introduction to Git and Github
• beginnerSoftware engineering Git Github Version control -
Training materials
Beginners introduction to Git and GitHub
• beginnerGit GitHub control version Reproducibility -
Adding Schema.org to a GitHub Pages site
schemaorg, TeSS, GitHub pages
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Training materials
Adding schema.org to a GitHub Pages site
• beginnerComputer science Mark-up Bioschemas Interoperability -
Presentation
Reproducible data analysis with RStudio, github and Rmarkdown
Data architecture, analysis and design Data management Data analysis
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slides
Slides for 'Contributing with GitHub via command-line' tutorial
contributing
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hands-on tutorial
Hands-on for 'Contributing with GitHub via its interface' tutorial
contributing
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hands-on tutorial
Hands-on for 'Contributing with GitHub via command-line' tutorial
contributing
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hands-on tutorial
Hands-on for 'Best practices for workflows in GitHub repositories' tutorial
fair ro-crate jupyter-notebook
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podcast, slides
RSE Byte-sized RSE Session 2: Collaboration and Code Review via GitHub
•• intermediateRSE Research software code review -
Tutorial
Contributing to the Galaxy Training Material - Contributing with GitHub via command-line
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Tutorial
Contributing to the Galaxy Training Material - Contributing with GitHub via its interface
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lessons, e-learning
Introduction to Data Management Practices - Versioning of data and code using Git
• beginnerData management FAIR data Software engineering RStudio CONVERGE README -
E-Learning, Training materials
Biology meets Programming - Introduction to Bioinformatics using Python
• beginnerBioinformatics Biology Python Python biologists Programming Data Analysis Sequence Analysis -
BD2K Data Science Open Educational Resources (OERs)
Ontology Biocuration Curation Identifiers Standards
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Video
A common framework for designing portable federated pipelines
•• intermediateData architecture, analysis and design data access federated data analysis -
Carpentries style curriculum
Introduction to Workflows with Common Workflow Language
• beginnerWorkflows RNA-Seq analysis cwl commonwl sciworkflows workflows -
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Extras
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Collaborating
Git
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Git
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Collaborating
Hg
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Hg
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Loops
Shell
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Make Reference
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Glittr.org
Glittr (https://glittr.org) is a web applications that helps you find and compare bioinformatics training material on GitHub and GitLab.
Glittr.org https://glittr.org https://tess.elixir-europe.org/content_providers/glittr-org Glittr (https://glittr.org) is a web applications that helps you find and compare bioinformatics training material on GitHub and GitLab. /system/content_providers/images/000/000/692/original/logo-with-domain.png?1698843802 -
Danish National Health Data Science Sandbox
The Health Data Science Sandbox is a national project coordinated by the Center for Health Data Science at the University of Copenhagen. Advisors and project data scientists are located at five Danish universities. We are building a data science sandbox for students and...
5 training materialsDanish National Health Data Science Sandbox https://hds-sandbox.github.io https://tess.elixir-europe.org/content_providers/danish-national-health-data-science-sandbox The Health Data Science Sandbox is a national project coordinated by the [Center for Health Data Science](https://heads.ku.dk/) at the University of Copenhagen. Advisors and project data scientists are located at five Danish universities. We are building a data science sandbox for students and researchers that contains non-person-sensitive datasets spanning key health data domains – electronic health records, omics data such as genomics and transcriptomics, images, and wearable device data. Datasets are sourced from public databases or generated via privacy-preserving approaches to synthetic health data. We are building modules that pair topical datasets with recommended analysis tools, pipelines, and learning materials/tutorials in a portable, containerized format. Our initial aim is to support university courses and programs in health data science and personal medicine, with broader environment access for researchers and university students planned in the future. Our sandbox for exploring health data science techniques will allow low-stakes guided learning and development followed by a smooth transition to a secure environment where users’ knowledge and tools can be applied to sensitive data. The sandbox environment is hosted on Danish supercomputers providing compute power while modules are publicly accessible on [GitHub](https://github.com/hds-sandbox). We thank the Novo Nordisk Foundation for funding support via the Data Science Research Infrastructure initiative. /system/content_providers/images/000/000/669/original/logo.png?1678825482