Difficulty level: Beginner
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
FAIR principles in practice for health data was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...
Scientific topics: Medical informatics, FAIR data, Data management, Computer science
Operations: Design, Standardisation and normalisation
Keywords: Clinical data, RDF, Knowledge graph, Semantic framework, FAIR, Findability, Accessibility, Interoperability, Reusability
Resource type: Video, E-learning
The questions this addresses are:
- Assembly: Is my genome assembly ready for scaffolding?
- Annotation: Is my genome assembly ready for structural annotation?
Keywords: assembly
Resource type: slides
In this course you will learn what type of information is stored in DisProt, gold standard resource of manually curated Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Regions (IDRs) from the literature. You will explore the main features of the database, its entries and...
Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis
Resource type: Webinar, Training materials
The questions this addresses are:
- How to perform functional annotation on protein sequences?
\nThe objectives are:
- Perform functional annotation using EggNOG-mapper and InterProScan
Keywords: genome-annotation, eukaryote
Resource type: hands-on tutorial
The questions this addresses are:
- How can we annotate a bacterial genome?
- How can we visualize annotated genomic features?
\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Prokka
- View annotations in JBrowse
Keywords: genome-annotation, prokaryote
Resource type: hands-on tutorial
The questions this addresses are:
- How to mask repeats in a genome?
- What is the difference between hard and soft-masking?
\nThe objectives are:
- Use Red and RepeatMasker to soft-mask a newly assembled genome
Keywords: genome-annotation, eukaryote
Resource type: hands-on tutorial
The questions this addresses are:
- What is a REST API?
- How to interact with Galaxy programmatically?
- Why and when should I use BioBlend?
\nThe objectives are:
- Interact with Galaxy via BioBlend.
Keywords: dev, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?
\nThe objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...
Keywords: assembly, prokaryote
Resource type: hands-on tutorial
The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?
\nThe objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.
Keywords: assembly
Resource type: hands-on tutorial
The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?
\nThe objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an...
Keywords: assembly
Resource type: hands-on tutorial
The questions this addresses are:
- How to generate a volcano plot from RNA-seq data?
\nThe objectives are:
- Create a volcano plot of RNA-seq data to visualize significant genes
Scientific topics: Transcriptomics
Keywords: transcriptomics
Resource type: hands-on tutorial
The questions this addresses are:
- What are the steps to process RNA-Seq data?
- How to identify differentially expressed genes across multiple experimental conditions?
- What are the biological functions impacted by the differential expression of genes?
\nThe objectives are:
- Check a...
Scientific topics: Transcriptomics
Keywords: transcriptomics, bulk, rna-seq, collections, drosophila, QC, cyoa
Resource type: hands-on tutorial
The questions this addresses are:
- What information can I get from a phylogenetic tree?
- How do I estimate a phylogeny?
\nThe objectives are:
- Understand the basic concepts behind phylogenetic trees, as applied to Mycobacterium tuberculosis
- Be able to read and interrogate a phylogeny...
Keywords: evolution, prokaryotes, phylogenetics, evolution, work-in-progress
Resource type: hands-on tutorial
The questions this addresses are:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?
\nThe objectives are:
- Choose your quantitation method.
Scientific topics: Proteomics
Keywords: proteomics, DDA
Resource type: hands-on tutorial
The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
\nThe objectives are:
- Protein identification from LC-MS/MS raw files.
Scientific topics: Proteomics
Keywords: proteomics, DDA
Resource type: hands-on tutorial
The questions this addresses are:
- How to perform label-free analysis in Maxquant?
- Which are the most abundant proteins in serum?
- How successful was the depletion of those in our experiment?
\nThe objectives are:
- Analysis of human serum proteome samples with label-free quantification...
Scientific topics: Proteomics
Keywords: proteomics, DDA, label-free
Resource type: hands-on tutorial
The questions this addresses are:
- How to download protein FASTA databases of a certain organism?
- How to download a contaminant database?
- How to create a decoy database?
- How to combine databases?
\nThe objectives are:
- Creation of a protein FASTA database ready for use with...
Scientific topics: Proteomics
Keywords: proteomics, DDA
Resource type: hands-on tutorial
The questions this addresses are:
- How to analyze metatranscriptomics data?
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?
\nThe objectives are:
- Choose the best approach to analyze metatranscriptomics data
...
Scientific topics: Metagenomics
Keywords: metagenomics, metatranscriptomics
Resource type: hands-on tutorial
The questions this addresses are:
- How to analyze metatranscriptomics data?"
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?
\nThe objectives are:
- Choose the best approach to analyze metatranscriptomics data
...
Scientific topics: Metagenomics
Keywords: metagenomics, metatranscriptomics
Resource type: hands-on tutorial
The questions this addresses are:
- How do I try to execute code, knowing it might fail?
- What are some situations where this is important?
- How can I write my own exceptions.
\nThe objectives are:
- catch an exception
- raise your own exception
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- How can I read from a file?
- How can I parse a CSV file?
- How can I write results out
\nThe objectives are:
- Read data from a file
- Write new data to a file
- Use with to ensure the file is closed properly.
- Use the CSV module to parse comma and...
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- How can I make a program do many things?
\nThe objectives are:
- Explain what for loops are normally used for.
- Trace the execution of a simple (unnested) loop and correctly state the values of variables in each iteration.
- Write for loops that use the...
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- How can my programs do different things based on data values?
\nThe objectives are:
- Write conditional statements including if, elif, and else branches.
- Correctly evaluate expressions containing and and or.
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- What kinds of data do programs store?
- How can I convert one type to another?
\nThe objectives are:
- Explain key differences between integers and floating point numbers.
- Explain key differences between numbers and character strings.
- Use built-in...
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- What all did I learn up until now?
\nThe objectives are:
- Recap all previous modules.
- Use exercises to ensure that all previous knowledge is sufficiently covered.
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- How do I write functions in Python?
- What is a function?
- What do they look like?
- Fill in the missing part of a function
\nThe objectives are:
- Understand the structure of a "function" in order to be able to construct their own functions and predict...
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- How do I do math in Python?
\nThe objectives are:
- Understand the fundamentals of object assignment and math in python and can write simple statements and execute calcualtions in order to be able to summarize the results of calculations and classify valid...
Keywords: data-science, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- What is a command shell and why would I use one?
- How can I move around on my computer?
- How can I see what files and directories I have?
- How can I specify the location of a file or directory on my computer?
- How can I create, copy, and delete files...
Keywords: data-science, bash, jupyter-notebook
Resource type: hands-on tutorial
The questions this addresses are:
- How can I calculate sums, averages, and other summary values?
- How can I combine data from multiple tables?
- How should I format data in a database, and why?
- How can I create, modify, and delete tables and data?
- How can I access databases from...
Keywords: data-science, SQL, jupyter-notebook
Resource type: hands-on tutorial