Bioinformatics training for every level

Create, customise, and maintain a Data Management Plan

This workshop will provide an overview of the Data Stewardship Wizard (DSW), a tool for creating and handling data management plans. This workshop was delivered as part of the 2026 edition of Digital Scholarship Days at the University of Oslo.

Applied Metagenomics - AM22 (October 11-14, 2022)

This course will give a comprehensive introduction to the research field of metagenomics. It will cover the basic concepts of microbiome analysis of shotgun metagenomic data using state of the art bioinformatics (amplicon sequencing will not be covered). The analysis methods that are being introduced are generic for all types of microbiomes, but we will be using data from the human microbiome as showcases. The course will start with the main preprocessing steps of raw sequence data, before various downstream analysis will be covered separately. These include taxonomic analysis, assembly, binning, and finally functional analysis with focus on antibiotic resistance genes. The theoretical part for each topic will be introduced via lectures, followed by practical hands-on exercises. **Target Audience** The course is intended for researchers and students that are, or are planning to work with data analysis of metagenomic data. **Software and Data** All software and databases together with the exercise data will be pre-installed on the course machines you will be using during the practical exercises of the course. All data can be downloaded locally through [data](https://gtpb.github.io/AM22/assets/data.zip) (Zipped file).

Applied Metagenomics - AM21 (November 1-5, 2021)

This course will give a comprehensive introduction to the research field of metagenomics. It will cover the basic concepts of microbiome analysis of shotgun metagenomic data using state of the art bioinformatics (amplicon sequencing will not be covered). The analysis methods that are being introduced are generic for all types of microbiomes, but we will be using data from the human microbiome as showcases. The course will start with the main preprocessing steps of raw sequence data, before various downstream analysis will be covered separately. These include taxonomic analysis, assembly, binning, and finally functional analysis with focus on antibiotic resistance genes. The theoretical part for each topic will be introduced via lectures, followed by practical hands-on exercises. **Target Audience** The course is intended for researchers and students that are, or are planning to work with data analysis of metagenomic data. **Software and Data** All software and databases together with the exercise data will be pre-installed on the course machines you will be using during the practical exercises of the course. All data can be downloaded locally through [data](https://gtpb.github.io/AM21/assets/data.zip) (Zipped file).

Genome assembly, annotation and comparative genomics - EBP-Nor workshop 2024

Training materials from the 3-day EBP-Nor Genome Assembly, Annotation and Comparative Genomics workshop that was given at the [Norwegian Biodiversity Genomics & Conference 2024](https://www.ebpnor.org/english/events/norwegian-biodiversity-and-genomics-conference-202.html). The repository includes slides and tutorials that covers the process from going from fastq files of your sequenced genome(s) to performing comparative gene analysis. #### Genome Assembly: The Genome Assembly section introduces participants to whole-genome assembly processes using real datasets. It includes: - **GenomeScope2**: Estimating genome size and heterozygosity. - **Smudgeplot**: Inferring ploidy levels from sequencing data. - **HiFiAdapterFilt**: Filtering adapters from PacBio HiFi reads. - **hifiasm**: Assembly of PacBio HiFi sequencing data. - **YaHS**: Scaffolding genome assemblies using Hi-C data. - **gfastats**: Assembly statistics and quality metrics. - **BUSCO**: Evaluating genome assembly completeness. - **Merqury**: Assessing genome assembly accuracy. - **FCS-GX and GRIT Rapid Curation suite**: Manual curation and contamination removal. - **PretextView**: Visualization of genome assemblies. #### Genome Annotation: Participants learn how to annotate genomes effectively through: - **RepeatMasker**: Masking genomic repeats. - **miniprot**: Mapping protein sets to genome assemblies. - **GALBA**: _Ab initio_ gene prediction. - **EvidenceModeler (EVM)**: Combining gene annotation evidence. - **BUSCO**: Evaluating annotation completeness. - **Functional annotation**: Assigning biological functions to genes. #### Comparative Genomics: This section provides practical training in comparative genomic analyses and visualization: - **OrthoFinder**: Identifying orthologous gene groups. - **R visualizations**: Basic visualization of OrthoFinder results. - **CAFE5**: Analysis of gene family evolution. - **GO enrichment analyses with g:Profiler**: Interpretation of functional enrichments using custom GO annotions.

Navigating Licensing in Bioinformatics: Software and Data Perspectives

This webinar reviews licensing for both software and data in bioinformatics research. We provide guidance on understanding different types of licenses, their implications, and best practices for selecting and applying them appropriately. Whether you're a researcher, bioinformatician, developer, or data steward, this webinar will equip you with the knowledge and tools necessary to navigate the complex landscape of licensing in bioinformatics effectively.

Life Sciences Research Data Management 2023 Course by ELIXIR Norway

Material from the Life Sciences 2023 RDM course.

Life Science RDM 2023 Course - Extended version in 6 modules

The material includes slides for all six modules covered for the Life Science RDM course 2023.

ELIXIR’s Impact Toolkit, to support performance and impact evaluation in a distributed data research infrastructure for the life sciences

This Toolkit collates a range of impact-related materials, including training documents and materials, worked examples, factsheets, lists of indicators, key publications, case studies, and presentation slides. These have been created and/or brought together using a bottom-up approach that tries to reflect the varied needs of Nodes in ELIXIR member countries. The primary audiences of this Toolkit are those in ELIXIR (e.g. operators, developers and managers of bioinformatics resources) wishing to demonstrate and communicate the performance, impact, and ultimately public value of their research infrastructure, to their particular set of funders and stakeholders. Sibling research infrastructures in the life sciences and beyond may also find the Toolkit useful.

ELIXIR-CONVERGE - The why of research data management

More and more funders require researchers to develop data management plans (DMPs). These plans should stimulate the researcher to consider from the beginning of the project to consider all aspects of data management. The video by ELIXIR-CONVERGE WP2 is a training material developed for researchers to learn about data management plans, from data stewards to FAIR principles.

Using the Norwegian e-infrastructure for Life Science and usegalaxy.no

The topic is on how you can use NeLS (nels.bioinfo.no) to store and share data, and to run analyses via customisable analysis workflows in usegalaxy.no. You will practice on transferring data between NeLS and usegalaxy.no, and to construct and run a complete sequence analysis workflow in usegalaxy.no.