Systems Biology services

Name Description ELIXIR Node

Cellular and molecular biology are fundamental to ELIXIR's mission. As part of our 2024–28 Programme, we are committed to advancing data services and software for research on nucleic acids, proteins and other biomolecules. This initiative will address new demands for multi-omics and multi-modal analyses, including imaging, by developing methods and partnerships. We will also expand expertise in reusable data and software to incorporate FAIR models, ensuring robust solutions for modelling at all scales. 

The following projects are key to connecting the latest developments with established data resources, unlocking the potential of cellular and molecular biology:

 ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI

This project aims to strengthen the basis for a one-stop shop connecting databases, datasets and tools for the deployment of the engineering Design-Build-Test-Learn (DBTL) framework in biotechnology. It will do so by surveying the tools and data landscape, pinpointing gaps and opportunities, and establishing design patterns for task-specific workflows for analysis, integration and sharing of multimodal data. 

It will provide a resource that will allow users to navigate the complex landscape of biotechnology tooling and data, as well as to establish solutions that fit their specific DBTL requirements. Use cases from ongoing programmes in various communities will be used to ascertain and establish the pragmatic value of the solutions. 

The work will be carried out through hands-on activities, dedicated workshops and hackathons, providing training and resources, as well as fostering industrial engagement. The experience of the communities and platforms involved in systems biology, industrial biotechnology, metabolic modelling, metabolomics, enzymes, bioprospecting and data management will be particularly valuable in this respect, as well as their respective industrial relations. Accordingly, the project engages participants from seven ELIXIR nodes and connects researchers and their activities from six communities. 

The project outcomes will contribute to advancing the ambition of connecting the latest developments and established data resources across ELIXIR to realise the potential of cellular and molecular biology, particularly in the fields of industrial biotechnology and biomanufacturing.

 ELIXIR Spain, ELIXIR Greece, ELIXIR France, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR UK
ELIXIR Finland, ELIXIR Germany, ELIXIR Netherlands, ELIXIR Slovenia, ELIXIR Sweden

The ELIXIR Metabolomics Community relies on standards, formats and data treatment solutions development and adoption, but it remains challenging to ensure high-quality reported metadata, sufficiently contextualised results, interoperable and reusable datasets and to integrate these metabolomics data with other omics or studies. 

This project is designed to address these issues and aims to connect key international standards with ELIXIR resources, as well as creating associated community guidelines and training materials. 

Based on the FAIRification framework, activities in the project will:

  • Increase interoperability and reuse of public metabolomics datasets and workflows through enhanced and extended open data standards, resources and new semantic annotations
  • Define, ensure and establish quality control for study baselines in Metabolomics and Exposomics
  • Facilitate metabolomic data interpretation and meta-analysis integration with multi-omics and systems biology studies

As a first necessary step, the project will create a Semantic Metabolomics Data Model to standardise metadata, ensuring unambiguous reuse of metabolomics projects. This model will focus on integrating key ontologies, providing open training initiative and enhancing the interoperability of metabolomics data through the production of open guidelines for annotation steps. By linking with ELIXIR’s Deposition databases, ISA Framework and other services, the project seeks to boost interconnection with ELIXIR platforms, other ELIXIR communities (Systems Biology, Food and Nutrition, Galaxy, Proteomics, Toxicology, Research Data Alliance Focus Group, etc.), the FAIR Cookbook and BioSchemas.org communities. Project outcomes are expected to promote  the emergence of ambitious and innovative semantic-based solutions for inter-comparison of studies in healthcare, clinical and plant domains.

 ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Italy, ELIXIR Spain, ELIXIR France, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR UK, EMBL-EBI

The Implementation Study aims to put into action priorities identified in the Community’s White Paper. It is divided into five Work Packages: 

  • WP0 for coordination.
  • WP1 aims to identify barriers to FAIRness in systems biology (SB) and medicine with emphasis on interoperability between models, data and tools.
  • WP2 presents three Use Cases (Metabolism in Health and Disease, in Toxicology, and in an Industry Setting) to identify potential ways forward.
  • WP3 concerns capacity building and training, since this area is often challenging for bench scientists.
  • WP4’s focus is to drive systems biology to translation and to build links with relevant industrial and societal sectors.

This work was presented in a series of webinars that are available here 

 ELIXIR Netherlands, ELIXIR Slovenia, ELIXIR Sweden, ELIXIR UK, ELIXIR Portugal, ELIXIR Luxembourg, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Greece, ELIXIR Norway