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1609 materials found

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

Cloud-SPAN Prenomics

Prenomics prepares learners for the Cloud-SPAN Genomics course. It teaches the basics of command-line programming, including: (1) file directory structure, (2) use of command-line utilities to connect to and use cloud computing and storage resources and (3) basic shell commands for file...

Scientific topics: Bioinformatics, Software engineering, Genomics

Operations: Query and retrieval, Data handling

Keywords: Cloud computing, Shell, Command line, Amazon Web Services, genomics, HPC, Data analysis, bioinformatics

Resource type: course materials, online course, Training materials

A Practical Guide for SARS-CoV-2 Whole Genome Sequencing Join now

Investigate SARS-CoV-2 sequencing methodologies
Using research, articles, and videos, you will access information and techniques to optimise your current data handling and processing. You will learn about sequencing platforms and library preparation methodologies, comparing the benefits and...

Keywords: Sequencing, Best Practices, quality control, Genomics, Metagenomics, Genomic data, library preparation, sars-cov-2, covid-19, surveillance

Resource type: FREE online course

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

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: Bioinformatics, Genomics

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: Genomics, Bioinformatics

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: Protein structure analysis, Machine learning, Structure prediction

Operations: Structure visualisation, Multiple sequence alignment

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?

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