This course will provide an introduction to metabolomics through lectures and hands-on sessions, using publicly available data, software, and tools. Participants will become familiar with standardised workflows as well as with the current state of experimental design, data acquisition (LC-MS, MS imaging), data processing and compound annotation, and modelling. In addition, they will learn about community standards and open data practices in metabolomics, particularly through the use of EMBL-EBI’s MetaboLights repository and Galaxy infrastructure. Participants will learn through hands-on tutorials how to use the tools available for data analysis and data submission. Additionally, case studies will be discussed to show how to employ the week’s learning.

Who is this course for?

This course is aimed at researchers who are new to the field of metabolomics and wish to learn about the process of conducting a metabolomics study. The course will benefit those who are planning to integrate metabolomics into their work, either moving into the field or as an investigator from other -omics. We will primarily focus on a basic introduction to metabolomics with worked examples using a predesigned LC-MS analysis workflow. Basic knowledge of programming languages can be an advantage (e.g. you understand the basic command line functioning, you can navigate Galaxy tutorials).

We recommend these free resources or other similar ones:

• The Unix Shell: https://swcarpentry.github.io/shell-novice/
• A Short Introduction to Galaxy: https://www.youtube.com/watch?v=IRdlOcVgjRY 

What will I learn?

Learning outcomes

After the course, you should be able to:

• Perform basic data processing, compound annotation, and modelling in metabolomics
• Estimate what factors contribute to designing a successful metabolomics study
• Describe the state-of-the-art in open science practices in metabolomics
• Access and use public metabolomics resources
• Cite the principles of creating a standardised workflow to perform metabolomics analysis

Course content

During this course, you will learn about: 

• Basic metabolomics experimental design, acquisition, and analysis
• Public metabolomics resources: Galaxy and MetaboLights
• Open source metabolomics tools made available through customisable workflows
• Case study based on a published/public example

Trainers

Please read our support page 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.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one 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 on 11 January 2026. Items marked * in the application are mandatory. Incomplete applications will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 26 January 2026. If you have any questions regarding the application process, please contact Juanita Riveros. 

Fees

 The registration fee includes:

• Catering as detailed on the course programme
• Accommodation for four nights (27, 28, 29, and 30 April)
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Secure virtual machines for the practical sessions listed in the programme
• Shuttle bus on the final course day to Cambridge train station 

* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Organiser for more information.

Financial assistance

Financial assistance is available to a limited number of participants attending this course.

Registration fee waivers

A limited number of registration fee waivers are offered for this course.

• Application process:
  • Apply for the fee waiver alongside your course application.
  • Provide a brief explanation of why you require the waiver and how attending the course will benefit your career.
• Notification:
  • You will be informed of your waiver status at the same time as the outcome of your course application.
  • If awarded, the registration fee will be waived entirely.

Travel grants

A limited number of travel grants of up to £1,000.00 are available to support participants' travel expenses.

• Covered expenses:
  • Airfare, train, bus, taxi, and visa costs.
• Application process:
  • Apply for the travel grant when submitting your course application.
  • You will be informed of the grant decision, including the amount awarded, along with your course application outcome.
• Reimbursement process:
  • Participants must pay upfront for their travel costs.
  • A reimbursement form will be provided upon course completion.
  • Submit the completed form with receipts within one month of travel completion.
• Grant adjustment:
  • The organisers may adjust the grant amount to accommodate more participants.

Financial assistance terms and conditions

• Selection process: Recipients of financial assistance will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not impact the outcome of your course application.

Additional information

Accommodation 

Hotel rooms will be provided on-site at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Course materials

The course materials from the 2025 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2026 edition.

Posters

All participants are expected to present a poster, and successful applicants will be asked to submit their poster upon registration. We expect the posters to act as a talking point between you, other participants, and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

Travel information

Electronic Travel Authorisations (ETAs) are needed for visitors to the UK who do not currently need a visa for short stays, or who do not already have a UK immigration status. Full details and information on how to apply can be found at the UK Gov website. 

Event terms and conditions

• Selection process: Recipients will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not affect your course application outcome.