Bioinformatics


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Courses tagged with "Bioinformatics"

GenEpi-BioTrain - Virtual training 09 & 10 - Unix for beginners & Introduction to the Conda ecosystem

 The aim of this virtual training is to introduce participants to working in Unix and creating Conda environments for running simple bioinformatics tasks. The training is divided into three sessions. In the first session, participants will be introduced to the Unix ecosystem and basic Unix commands useful for inspecting various files. In the second session, participants will focus on file manipulation and consolidate their understanding of the command line interface. The third session aims to enhance participants’ ability to perform bioinformatics tasks in the command line by setting up and using Conda environments.


Duration: Three half-days on 20, 21 and 22 August 2024 from 10:00 to 14:00 (CET)


Location: Online - Find the link after enrolment. 


Audience: Public health microbiologists, epidemiologist, or beginners in bioinformatics interested in learning about the power of the command line interface and setting up separate environments with bioinformatics tools.


Objectives:  

Upon completion of this workshop, participants will be able to:

  • Understand and recognize Unix as an ecosystem
  • Execute several basic commands in the terminal
  • Navigate in Unix
  • Run simple commands for inspecting files
  • Manipulate file contents from command line
  • Understand the differences between file locations and running commands in the terminal
  • Understand principles behind package management in separate environments
  • Have a basic understanding of the Conda ecosystem for handling environments and packages
  • Download and install Mamba on Ubuntu
  • Use Mamba - A Conda ecosystem package manager
  • Create and activate environments
  • Install a bioinformatics software
  • Run a bioinformatics analysis

Participation: This course is open for public enrolment from 29 July 2024.

Category: 2024 Catalogue
GenEpi-BioTrain - Virtual training 16 - Building bioinformatics workflows

 The aim of this virtual training is to provide learners with skills to create and maintain workflows for automating routine bioinformatics tasks.


Duration: Two half-days on 19 and 21 March 2025 from 09:00 to 12:30 (CET)


Location: Online - Find the link after enrolment. 


Audience: Beginners in bioinformatics, who have some familiarity with navigating and interacting with Unix terminals, creating and running simple bash scripts, and creating and working with virtual environments through the Conda ecosystem.


Objectives:  

Upon completion of this virtual training, participants will be able to:

    • Execute bioinformatics commands from environments, without activating them
    • Describe how to work with positional arguments
    • Define the basic concepts behind modularisation of workflows
    • Convert bioinformatics commands into a modular structure of scripts
    • Generate a main script that executes each module with positional arguments
    • Individually expand their workflows with new modules

Participation: This course is open for public enrolment.

Category: 2025 catalogue
GenEpi-BioTrain - Virtual training 17 - Nanopore Sequencing Technology

 The aim of this virtual training workshop is to provide participants with a comprehensive understanding of Nanopore sequencing technology, from its underlying principles to its practical applications in epidemiological surveillance of infectious diseases. The webinar will enable participants to explore the latest advancements in Nanopore technology, develop key bioinformatics skills for analysing Nanopore sequencing data, and understand its diverse applications in fields such as virology, bacteriology, and mycology. In this virtual training, a focus will be given on applications to the surveillance and outbreak investigation of pathogens.


 Dates and Duration: 9 and 11 April 2025. Two half-days 09:30-12:00 CET. 


Location: Online - Find the link after enrolment. 


Audience: Public health microbiologists, epidemiologist, or bioinformaticians interested in learning about nanopore sequencing technology.

The practical exercise in this webinar has several prerequisites and requires software installation. Please follow the 'Prerequisites' and 'Software Requirements' sections carefully.

Objectives:  

Upon completion of this workshop, participants will be able to:

    • Understand the basic principles of Nanopore sequencing
    • Discuss the latest advancements in Nanopore technology
    • Perform bioinformatics analyses using Nanopore data
    • Apply Nanopore sequencing in various areas
    • Recognize the strengths and limitations of Nanopore sequencing 

Participation: This course is open for public enrolment.

Category: 2025 catalogue
GenEpi-BioTrain - Virtual training 15 - Focus on the Agents of Diphtheria

The aim of this virtual training is to provide participants with in-depth knowledge of the agents causing diphtheria, and their diagnosis, clinical definition, antibiotic resistance and taxonomy. Diphtheria surveillance, vaccination strategies, and treatment protocols will also be covered. This webinar will also allow participants to gain practical bioinformatics skills for genotyping C. diphtheriae and C. ulcerans strains.


 Dates and Duration: March 5th and 7th morning, 2025. Two half-days. 


Location: Online - Find the link after enrolment. 


Audience: Public health microbiologists, epidemiologists, and bioinformaticians interested in diphtheria. 

Objectives:  Upon completion of this workshop, participants will be able to:

    • Understand which are the causative agents of diphtheria
    • Learn about diagnostic techniques and clinical definition of diphtheria
    • Perform genotyping of C. diphtheriae and C. ulcerans strains for epidemiological surveillance and outbreak investigation
    • Understand antibiotic resistance breakpoints and resistance patterns of diphtheria agents.
    • Understand diphtheria surveillance at national and international scales
    • Gain knowledge about prevention, case management and transmission control approaches, including vaccination, antibiotic treatment and diphtheria antitoxin use.

Participation: This course is open for public enrolment 2 weeks in advance.

Category: 2025 catalogue
GenEpi-BioTrain - Virtual training 14 - R data analysis and visualisation for beginners

 R is an open source software, a widely used programming language for statistical data analysis and a powerful tool for visualisation. The aim of this virtual training is to introduce participants to data analysis and plotting in R. 

The training is divided into four sessions:

  1. In the first session, participants will be introduced to the Rstudio environment and will acquire a strong understanding of basic data types and structures in R. 
  2. The second session will focus on downloading libraries, importing data and basic commands and concepts in manipulating dataframes using base R and tidyverse packages. 
  3. The third session will introduce participants to functions and a number of plotting methods for different kinds of data visualisation. 
  4. The fourth session will summarize content learned in the previous three sessions by conducting a small analysis of a dataset using the previously taught tools.
Note that you will need to have both R and RStudio preinstalled and running on your PC. You will receive more information on how to install both programs once you are enroled.


Duration: Four half-days of 3-4 hours duration, with interactive classes and small assignments in between, during the week 17-20 February 2025.


Location: Online - Find the link after enrolment.


Audience: Public health microbiologists, epidemiologist, or beginners in bioinformatics interested in learning about R programming for data visualisation.

Learning objectives:  

    • Install and understand the R programming language and the Rstudio shell.
    • Import and export data to R.
    • Manipulate data objects in R.
    • Visualise data using base plotting in R.
    • Understand how different visualisations aid in interpretation of data.
    • Conduct simple analysis of resistance increase over time OR exploratory data analysis of WHO tuberculosis dataset.

Participation: This course is open for public enrolment.

Category: 2025 catalogue
Podcast: A closer look at viruses
This podcast presents an introduction to virology, genetic epidemiology and bioinformatics. In this episode, ECDC’s expert in genetic epidemiology and bioinformatics – Theresa Enkirch gives us an overview of what genetic epidemiologists and bioinformaticians do and how that has changed the current epidemiological world. She also talks about a brand new ECDC course – the GenEpiBioTrain – that can properly boost one’s knowledge about all matters regarding bioinformatics and genetic epidemiology. 


Duration: 20 minutes 


Audience: general public 


Participation:  This podcast is open for public. 

GenEpi-BioTrain - Virtual Training 03: Introduction to bioinformatic analysis of SARS-CoV-2 amplicon sequencing data

The aim of this virtual training is to introduce participants to theoretical and practical aspects of analysing SARS-CoV-2 amplicon sequence data (mainly ARTIC amplicon panels) from single patient samples. Participants will get insights into the background of amplicon panels, analysis steps and tools, as well as data quality control.


Duration: Two half-days on 25 and 26 September 2023


Location: Online - Find the link after enrolment. 


Audience:  Experts interested in analysing amplicon sequencing data of SARS-CoV-2 with the DRAGEN COVID Lineage on the Illumina BaseSpace cloud. A free Illumina BaseSpace account is required and should be registered before the training.


Objective:  After completing this training, you will be able to conduct a basic analysis of SARS-CoV-2 amplicon sequencing data to detect mutations and determine the variant. You will have a basic understanding of the analysis steps and quality control parameters.


Participation: The recordings of this course are open for public enrolment.

GenEpi-BioTrain - Training Materials on Phylogeny for FWD surveillance

You will find course material that you may use to offer a training for your target audience. Your target audience could include beginners in bioinformatics or public health professionals, who are expected to have a future role in using whole-genome sequencing for public health and pathogen surveillance 


Audience:  Trainers in introduction to Genomic Epidemiology and Public Health Bioinformatics.


Objectives: 

Learning objectives of the training material include:

      • Displaying, manipulating, and interpreting phylogenetic trees
      • Extracting meaningful insights into the genetic diversity, population structure, and evolutionary history of pathogens relevant to FWD surveillance.
      • Identifying genetic variations among pathogens associated with FWD (alignment of DNA or protein sequences)
      • Finding the best evolutionary model for Maximum-Likelihood (ML) analyses for accurately reconstructing evolutionary relationships among pathogens
      • Being able to identify genetic relatedness and transmission patterns of FWD pathogens (using distance or ML methods) 
      • Constructing temporally informative phylogenetic trees by evaluating the clock signal in phylogenetic data and applying time-scaling techniques


Access: These course materials are open for public, regardless of people intending to teach the topic or learn form the materials in a self-study modality.


Category: Course Packages
GenEpi-BioTrain - Training Materials on Genomic Epidemiology and Public Health Bioinformatics - Bridging the gaps

You will find course material that you may use to offer a training for your target audience. Your target audience could include beginners in bioinformatics or public health professionals, who are expected to have a future role in using whole-genome sequencing for public health and pathogen surveillance 


Audience:  Trainers in introduction to Genomic Epidemiology and Public Health Bioinformatics.


Objectives: 

Learning objectives of the training material include:

    • Process sequencing data (from raw data to genomes)  
    • Critically evaluate data quality at all steps of the process 
    • Write basic python/bash scripts, to extract relevant information from processed data 
    • Write a basic processing pipeline 
    • Understand the importance and underlying principles of good coding practice, code documentation and code sharing 
    • Perform basic analysis supporting epidemiological investigations, including interaction with public databases 


Access: These course materials are open for public, regardless of people intending to teach the topic or learn form the materials in a self-study modality.


Category: Course Packages
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