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155 materials found

Difficulty level: Intermediate 


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 '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 - 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

RDMbites: Image data

The RDMbites collection to learn to manage biological image data

Keywords: imaging, 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

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 '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

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

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

Resource type: Poster

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: Metatranscriptomics, Sample collections, Metabolomics, Metagenomics

Keywords: hologenomics, metagenomics, Metabolomics, MGnify, Workshop

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

Exploring structural and functional annotations of IDPs with DisProt

In this course you will learn how to explore a DisProt entry, along with its main features (structural and functional annotations). You will also learn how to search the database for specific annotated aspects and how to download the output of a search.

Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis

Resource type: Webinar, Training materials

Hands-on for 'Genome Assembly Quality Control' tutorial

The questions this addresses are:
- Is my genome assembly ready for annotation and/or scaffolding?

The objectives are:
- Assess assembly quality

Keywords: assembly, assembly, quality control

Resource type: hands-on tutorial

Hands-on for 'Refining Genome Annotations with Apollo (eukaryotes)' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, eukaryote, cyoa

Resource type: hands-on tutorial

Hands-on for 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial

The questions this addresses are:
- How can we extract annotated allelic variants in SARS-Cov-2 sequences in Galaxy?
- Which tools and workflows can we use to identify SARS-CoV-2 lineages in Galaxy?

The objectives are:
- Repeat SARS-CoV-2 data preparation
- Select and run workflow to...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'M. tuberculosis Variant Analysis' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from M. tuberculosis (Mtb) and the Mtb reference genome

The objectives are:
- How should we filter those variants
- How can we predict drug resistance from those variants
- How do we annotate those...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Refining Genome Annotations with Apollo (prokaryotes)' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker (short)' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome?
- How to evaluate and visualize annotated genomic features?

The objectives are:
- Load genome into Galaxy
- Annotate genome with Maker
- Evaluate annotation quality with BUSCO
- View annotations in JBrowse

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Funannotate' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome with Funannotate?
- How to perform functional annotation?
- How to evaluate and visualize annotated genomic features?
- How to format the annotation for submission at NCBI?

The objectives are:
- Load genome into...

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial

The questions this addresses are:
- How can a genome of interest be assembled against a background of contaminating reads from other genomes?
- How can sequencing data from public sources be turned into assembly-ready polished datasets?

The objectives are:
- Obtain viral (SARS-CoV-2)...

Keywords: assembly, covid19

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

The objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality of...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'Genome assembly using PacBio data' tutorial

The questions this addresses are:
- How to perform a genome assembly with PacBio data ?
- How to check assembly quality ?

The objectives are:
- Assemble a Genome with PacBio data
- Assess assembly quality

Keywords: assembly, assembly, pacbio

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline - short version' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

The objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality of...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with Volcano Plot in R' tutorial

The questions this addresses are:
- How to customise Volcano plot output in R?

The objectives are:
- Learn how to use R to edit Volcano plot colours, points, labels and categories

Scientific topics: Transcriptomics

Keywords: transcriptomics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Identifying tuberculosis transmission links: from SNPs to transmission clusters' tutorial

The objectives are:
- Create a SNP alignment
- Calculate pairwise SNP distances between MTB samples
- Identify transmission clusters based on SNP distances
- Study the emergence and spread of drug resistance based on transmission analysis.

Keywords: evolution

Resource type: hands-on tutorial

Hands-on for 'Introduction to Machine Learning using R' tutorial

The questions this addresses are:
- What are the main categories in Machine Learning algorithms?
- How can I perform exploratory data analysis?
- What are the main part of a clustering process?
- How can a create a decision tree?
- How can I assess a linear regression model?

The...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 3: Taxonomy' tutorial

The questions this addresses are:
- How do I look at differentially expressed taxa?
- Can we get top 5 or 10 taxa present in the sample?
- How can I visualize my results?

The objectives are:
- A taxonomy and quantitational analysis of metaproteomic mass spectrometry data.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Secretome Prediction' tutorial

The questions this addresses are:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?

The objectives are:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by...

Scientific topics: Proteomics

Keywords: proteomics, human

Resource type: hands-on tutorial