Register training material
476 materials found

Content provider: Galaxy Training 


Hands-on for 'Avian influenza viral strain analysis from gene segment sequencing data' tutorial

The questions this addresses are:
- With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?
- Is it possible to reuse existing...

Scientific topics: Genetic variation

Keywords: variant-analysis, virology, public health, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'Python - Coding Style' tutorial

The questions this addresses are:
- Why should you follow software code style conventions?
- Who is setting code style conventions?
- What code style conventions exist for Python?

The objectives are:
- Understand the benefits of following community coding conventions

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Visualize EBV cube data with Panoply netCDF viewer' tutorial

The questions this addresses are:
- How to start Panoply interactive environment in Galaxy?
- How to inspect EBV cube netCDF data?
- How to make a plot with Panoply?
- Where to save your plots in Panoply?
- How to customize plots in Panoply?
- How to generate animation in Panoply?

The...

Scientific topics: Ecology

Keywords: ecology, interactive-tools, EBV cube, Data visualization

Resource type: hands-on tutorial

Hands-on for 'Cleaning GBIF data for the use in Ecology' tutorial

The questions this addresses are:
- How can I get ecological data from GBIF?
- How do I check and clean the data from GBIF?
- Which ecoinformatics techniques are important to know for this type of data?

The objectives are:
- Get occurrence data on a species
- Visualize the data to...

Scientific topics: Ecology

Keywords: ecology, gbif, data management, data cleaning

Resource type: hands-on tutorial

Hands-on for 'Visualization of Climate Data using NetCDF xarray Map Plotting' tutorial

The questions this addresses are:
- What is xarray map plotting?
- How to plot NetCDF data using xarray map plotting tool?
- What are the different types of projections and colormap options available in the tool?

The objectives are:
- Learn about plotting Climate Data
- Learn about NetCDF...

Scientific topics: Ecology

Keywords: ecology, pangeo

Resource type: hands-on tutorial

Hands-on for 'Preparing genomic data for phylogeny reconstruction' tutorial

The questions this addresses are:
- How do I find a set of common proteins (orthologs) across related species or strains?
- How do I organize a set of orthologs to infer evolutionary relations between species or strains (phylogenetic reconstruction)?

The objectives are:
- Mask repetitive...

Scientific topics: Ecology

Keywords: ecology, phylogeny, data handling, functional annotation

Resource type: hands-on tutorial

Hands-on for 'Teaching Python' tutorial

The questions this addresses are:
- What methods can I incorporate to improve student material uptake within my python courses?
- How do I write problems that use these methodologies

The objectives are:
- Learn about four different problem design ideas, and one teaching methodology.

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Virtual Environments For Software Development' tutorial

The questions this addresses are:
- What are virtual environments in software development and why you should use them?
- How can we manage Python virtual environments and external (third-party) libraries?

The objectives are:
- Set up a Python virtual environment for our software project...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Type annotations' tutorial

The questions this addresses are:
- What is typing?
- How does it improve code?
- Can it help me?

The objectives are:
- Understand the utility of annotating types on one's code
- Understand the limits of type annotations in python

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Conda Environments For Software Development' tutorial

The questions this addresses are:
- What are Conda environments in software development and why you should use them?
- How can we manage Conda environments and external (third-party) libraries via Conda?

The objectives are:
- Set up a Conda environment for our software project using...

Keywords: data-science, conda, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Multiprocessing' tutorial

The questions this addresses are:
- How can I parallelize code to make it run faster
- What code is, or is not, a prime target for parallelisation

The objectives are:
- Understanding how to paralellise code to make it run faster.
- Identifying how to decompose code into a parallel unit.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Testing' tutorial

The questions this addresses are:
- Does the code we develop work the way it should do?
- Can we (and others) verify these assertions for themselves?
- To what extent are we confident of the accuracy of results that appear in publications?

The objectives are:
- Explain the reasons why...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

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

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?

The objectives are:
- Identify which operations to perform...

Scientific topics: Transcriptomics

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

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?

The objectives are:
- Become familiar with...

Scientific topics: Transcriptomics

Keywords: single-cell

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?

The 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 ?

The 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?

The 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?

The 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?

The 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?

The 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?

The 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?

The 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?

The 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?

The 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

The 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?

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

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

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?

The objectives are:
- Setup a tailnet across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial