Resources and Trainings Online

This course is designed to describe and illustrating the main steps of analysing mRNA-sequencing data from raw data (fastq files) up to the functional analysis of differentially expressed genes.

Attendees should have a basic level of LINUX and R.

or: What can I do at the black screen?

Lennart C. Karssen 

Table of contents from the workshop that took place at the International Centre for Theoretical Physics, Trieste, Italy

The field of metagenomics and whole community sequencing is a promising area to unravel the content of microbial communities and their relationship to disease and antimicrobial resistance in the human population. Bioinformatic tools are extremely important for making sense out of metagenomics data, by estimating the presence of pathogens and antimicrobial resistance determinants in complex samples. Combined with relevant explanatory data, metagenomics is a powerful tool for surveillance.

In this course, we teach about the potential of metagenomics for surveillance and give the learners an overview of the steps and considerations in a metagenomics study. After this course, the learners will know: - the difference between the concepts of metagenomics and other microbial genomics - the need to use controls in different steps of a metagenomics study - the advantages of metagenomics for the surveillance of antimicrobial resistance - how sampling design, sample size, sample material and sample handling influence the outcome of a metagenomics study - sample processing for bacterial and viral metagenomics - different sequencing platforms and their possibilities regarding metagenomics - the steps involved in a general metagenomics study, including quality control, mapping to different databases, and read count analysis - the principles behind various tools available for analysis of metagenomics data - how to interpret read classification results - the need for epidemiology in surveillance - the concept of global and integrated surveillance - the challenges for the use of metagenomics in surveillance - the potential of metagenomics for surveillance We look forward to welcoming you !

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses

Here you will find a CRG course and tutorial material for the Parallel distributed computational workflows with Nextflow and Docker containers course

As you know, our summer school NGSchool: Statistical Learning in Genomics has been moved to 2021, but this year we are organizing a series of programming workshops in bioinformatics.

First series of online workshops will start in mid-June and they will be held on Thursdays. Webinars will last 1.5-2 hours and there will be a live broadcast when you will be able to ask questions to the speakers. Later the webinars will be also available through our Youtube channel. Below you will find the calendar of our webinars and information about speakers. Soon we will announce more details, so stay tuned!

Faced with the significant change in the way schools and schooling are now being operated in Australia and around the world, teachers are being asked to reskill at an unprecedented pace.

In-service teachers can be left feeling somewhat uncertain about how best to develop online lessons for their students when taken out of the familiar environment of a physical classroom. This course aims to be equally useful for pre-service teachers at a time when teaching practice is becoming increasingly digitised.

This course is a rapid-fire introduction to remote/online learning. It is light on theory and rich in practical advice and exemplars. Remote learning is possible, fun and challenging!

Each of the three modules in the course is designed to take around an hour to complete, and you are encouraged to use the forums along the way to share ideas, questions, and activities with each other.

Easily digestible modules will explore different aspects of Open Science and allow life sciences researchers to gain an ‘Open Science Expert’ Certificate, with prizes for the most active participants. You will learn online with many interactive elements and loads of multimedia content. Each week will have a specific focus and give an insight to the different aspects of Open Science.

You can listen to the podcast HERE

Description of the e-learning course

Background

The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases.

The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study.

Goal

The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships.

Target audience

Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology.