Content provider: Galaxy Training
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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