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Hands-on for 'Somatic Variant Discovery from WES Data Using Control-FREEC' tutorial

The questions this addresses are:
- What are the specific challenges in locating human Copy Number Variances (hCNVs)?
- How to preprocess the sequenced reads for hCNVs detection?
- How can you detect the hCNVs in/from tumor and normal tissue of the same individual?
- How can you visualise...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

RDMbites: Image data

The RDMbites collection to learn to manage biological image data

Keywords: imaging, data management

Resource type: Video

RDMbites: Sensitive data

The RDMbites playlist for learning how to manage sensitive data.

Keywords: sensitive data, data management

Resource type: Video

RDMbites: Sequencing data

The RDMbites collection to learn how to manage sequencing data

Keywords: transcriptomics, FASTQ, FastQC, Sequencing

Resource type: Video

RDMbites: REDCap

The RDMbites collection to learn how to use advanced functionality in REDCap, a browser-based, metadata-driven EDC software and workflow methodology for designing clinical and translational research databases.

Keywords: REDCap, sensitive data, data management

Resource type: Video

The essentials of DUO codes

The European Genome-phenome Archive (EGA) offers permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data from research projects and healthcare studies.

During this webinar, the speaker will:
- Introduce the audience to...

Scientific topics: Genomics, Bioinformatics

Keywords: bioinformatics, Genomics

Resource type: Video

Introduction to the EGA and its Ecosystem of Tools

The European Genome-phenome Archive (EGA) is a resource for archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and...

Scientific topics: Bioinformatics, Genomics

Keywords: e-learning, bioinformatics, Genomics

Resource type: Video

Prediction of protein structures and complexes with AlphaFold on the HPC

At the end of 2020, results for the CASP14 (Critical Assessment for protein Structure Prediction) were released. Just like in 2018, DeepMind Technologies won the competition with their deep (machine) learning based AlphaFold prediction models. However, the leap in prediction accuracy now raised...

Scientific topics: Structure prediction, Machine learning, Protein structure analysis

Operations: Multiple sequence alignment, Structure visualisation

Keywords: AlphaFold Database (13181), Structure prediction

Resource type: Slideshow, Training materials

Hands-on for 'Trajectory Analysis using Monocle3 ' tutorial

The questions this addresses are:
- How can I prepare input files for Monocle starting from an AnnData object?
- How can I infer lineage relationships between clusters, without a time series?
- What can trajectory analysis tell us?

\nThe objectives are:
- Identify which operations to...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, trajectory-analysis, paper-replication

Resource type: hands-on tutorial

Slides for 'Trajectory analysis' tutorial

The questions this addresses are:
- What is trajectory analysis?
- What are the main methods of trajectory inference?
- How are the decisions about the trajectory analysis made?
- What to take into account when choosing the method for your data?

\nThe objectives are:
- Become familiar with...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Hands-on for 'Identification of the micro-organisms in a beer using Nanopore sequencing' tutorial

The questions this addresses are:
- How can yeast strains in a beer sample be identified?
- How can we process metagenomic data sequenced using Nanopore?

\nThe objectives are:
- Inspect metagenomics data
- Run metagenomics tools
- Identify yeast species contained in a sequenced beer sample...

Scientific topics: Metagenomics

Keywords: metagenomics, nanopore, beer, citizen science, metagenomics

Resource type: hands-on tutorial

Hands-on for 'Evaluating and ranking a set of pathways based on multiple metrics' tutorial

The questions this addresses are:
- How to evaluate a set of heterologous pathways ?

\nThe objectives are:
- Calculate the production flux of the lycopene target molecule using Flux Balance Analysis tool.
- Compute thermodynamics values to optimize the yield of the reaction producing the...

Keywords: synthetic-biology

Resource type: hands-on tutorial

Hands-on for 'Long non-coding RNAs (lncRNAs) annotation with FEELnc' tutorial

The questions this addresses are:
- How to annotate lncRNAs with FEELnc?
- How to classify lncRNAs according to their localisation and direction of transcription of proximal RNA transcripts?
- How to update genome annotation with these annotated lncRNAs?

\nThe objectives are:
- Load data...

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Teaching online' tutorial

The questions this addresses are:
- What are the different ways of teaching online?
- How Galaxy can be used to teach online?

\nThe objectives are:
- List different ways to teach online
- Use Galaxy to teach online

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Hybrid training' tutorial

The questions this addresses are:
- What is hybrid training?
- How to deliver hybrid training using Galaxy?
- What should be prepared for an hybrid training event?

\nThe objectives are:
- Describe hybrid training
- Organize an hybrid training event using Galaxy

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Motivation and Demotivation' tutorial

The questions this addresses are:
- What is motivation and demotivation?
- How do motivation and demotivation impact learning processes?
- What can instructors do to motivate learners?

\nThe objectives are:
- List factors of motivation and demotivation
- Identify what instructors can do to...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Training techniques to enhance learner participation and engagement' tutorial

The questions this addresses are:
- What does make a training effective?
- How can instructors enhance learner participation and engagement?

\nThe objectives are:
- Describe what makes training effective
- Describe what makes a trainer effective
- Identify some strategies that facilitate...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Teaching experiences' tutorial

The questions this addresses are:
- How to teach using Galaxy?
- What are the different practises?

\nThe objectives are:
- Learn how others teach using Galaxy

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Live Coding is a Skill' tutorial

The questions this addresses are:
- Why do we teach programming using participatory live coding?

\nThe objectives are:
- Explain the advantages and limitations of participatory live coding.
- Summarize the key dos and do nots of participatory live coding.
- Demonstrate participatory live...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Assessment and feedback in training and teachings' tutorial

The questions this addresses are:
- What are the different types of feedback?
- When do get and receive feedback?
- For which purpose do we need feedback?

\nThe objectives are:
- Describe the differences between formative and summative assessment
- Explain why frequent feedback is...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Upload data to Galaxy' tutorial

The questions this addresses are:
- How to upload data to Galaxy

\nThe objectives are:
- Learn how to upload a file by pasting in a URL
- Learn how to import data from a shared library
- Determine the best strategy to get data into Galaxy

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'Design and plan session, course, materials' tutorial

The questions this addresses are:
- Is the structured approach to course design?
- How to articulate learning outcomes commensurate with the cognitive complexity of the target learning?
- How to devise learning experiences and course content?
- What are the steps that can help trainers...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Principles of learning and how they apply to training and teaching' tutorial

The questions this addresses are:
- What are the main principles that drive learning?
- How can these principles be applied to training and teaching?

\nThe objectives are:
- Describe how learning works according to a few learning models
- Explain how learning models can help you improve...

Keywords: contributing

Resource type: hands-on tutorial

Slides for 'Overview of the Galaxy Training Material for Instructors' tutorial

The questions this addresses are:
- How can I use the GTN for teaching?
- What resources are available?
- Why is it a good choice?

Keywords: teaching

Resource type: slides

3DBionotes COVID-19 Structural Hub: A Central Resource for Validation Information and Refined Models

Poster presented at the 21st European Conference on Computational Biology (ECCB 2022), celebrated in Sitges, Spain, 12-21 September 2022.

Scientific topics: Data mining, Data integration and warehousing, Data visualisation, Structural biology

Keywords: covid-19, Structural biology, Protein models, electron microscopy, data annotation, Web Services (5596), Quality Validation, Cryo-Electron Microscopy

Resource type: Poster

Hands-on for 'Deploying Tailscale/Headscale for private mesh networking' tutorial

The questions this addresses are:
- What is Tailscale?
- When is it useful?
- Is it right for me?

\nThe objectives are:
- Setup a tailnet across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial

Hands-on for 'Deploying Wireguard for private mesh networking' tutorial

The questions this addresses are:
- What is wireguard?
- When is it useful?
- Is it right for me?

\nThe objectives are:
- Setup a wireguard mesh across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial

Intermediate Research Software Development Skills In Python

This is a multi-day, intermediate-level lesson/course in software development skills for researchers using Python as a programming language. A typical learner for this course may be someone who is working in academic research and, needing to write some code, has gained basic software development...

Keywords: intermediate, Coding, software engineering, Carpentries Incubator

Organisation and utilisation of hologenomic datasets – course notes

This course covered the generation and application of large-scale holo-omic data sets, such as those produced within the HoloFood project. This course was run in September 2022, in-person in Bilbao, as part of the 1st Applied Hologenomics Conference. These course notes include the lecture slides...

Scientific topics: Metagenomics, Metabolomics, Sample collections, Metatranscriptomics

Keywords: hologenomics, metagenomics, Metabolomics, MGnify, Workshop

Resource type: Slides, course materials, hands-on tutorial

WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.

Event description 

Bioinformatics workflows can...

Keywords: Bioinformatics, Workflows, Nextflow, Containerisation