Run jointly with SymbNET, this virtual course will introduce and discuss state-of-the art tools for understanding microbial communities (metagenomics) and discovering and analysing species interactions in gut microbial communities, with a particular focus on metabolic interactions. The goal will be to enable users to integrate experimental results with the latest computational methods to move from correlative analyses of host-microbiome systems towards mechanistic understanding, using a combination of introductory lectures and hands-on training materials.

Virtual course

Participants will learn via a mix of pre-recorded lectures, live presentations, trainer Q&A sessions and hands-on training. Live sessions will be delivered using Zoom with additional support and communication via Slack. 

Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their machines.

Participants will need to be available between the hours of 09:00-17:30 GMT each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times.

About SymbNET

SymbNET is a European network for host-microbe interactions research, funded by the European Union’s Horizon 2020 research and innovation programme. The project coordinated by FCG-IGC (Instituto Gulbenkian de Ciência, Portugal), brings together the world-leading research institutions EMBL (European Molecular Biology Laboratory, Germany),  CAU (Christian-Albrechts-Universität zu Kiel, Germany),  and UNIL (Université de Lausanne,  Switzerland), and a local widening partner ITQB NOVA (Instituto de Tecnologia Química e Biológica, Portugal).

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement Nº 952537 

Who is this course for?

This course is aimed at those wishing to undertake analysis of microbial communities, with a particular emphasis on understanding the interactions and cross-talk of community members, especially using metabolomics.  Participants are expected to have a good understanding of microbiology, metagenomics and/or metabolomics. Familiarity with Unix is a requirement, as is general use of bioinformatics tools.
 

15 places are reserved for SymbNET members. Participants from SymbNET institutes will be entitled to free registration. For any enquiries, please contact symbnet@igc.gulbenkian.pt

What will I learn?

Learning outcomes

• Access and retrieve information from metagenomics, metabolomics, and genome-scale metabolic modelling resources
• Apply metagenomics, metabolomics and data integration analysis pipelines
• Identify and analyse experimental and computational challenges in metagenomics and metabolomics experiments
• Evaluate the utility of metagenomics and metabolomics integration methods for different research objectives
• Design metabolomics and metagenomics experiments and data analysis workflows

Course content

During this course you will learn about:

• Metagenomics analysis: MetaSPAdes, MetaPlasmidSPAdes, VIRifyMetagenomics resources: MGnify
• Metabolomics analysis: Agilent Qual, Quant, Mass Profiler Professional, metaBUNT
• Metabolomics resources: MetaboLights, KEGG, Human Metabolome DataBase (HMDB)
• Metagenomics and metabolomics integration resources: Virtual Metabolic Human (VMH), EMBL_GEMS
• Metagenomics and metabolomics integration tools: CarveME, metaGEM, SMETANA

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form, providing answers as directed
   
• Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs that cover your:
  • scientific biography/work experience
  • current research interests
     
• Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by 23:59, Monday 6 December 2021.

Incomplete applications will not be considered.

Everybody who applied before 6 December 2021 will be informed of the status of their application (successful, waiting list, rejected) by Monday 10 January 2022.

Posters presentation

All participants will be asked to present a poster about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Further details will be provided following registration.