Systems biology: bridging the gap to industry needs

An aim of systems biology is to understand biological functions by modelling metabolic interactions and processes. Different modelling techniques have been developed and applied. Out of these, the use of genome-scale metabolic models (GEMs) stands out as a widely applicable approach ranging from optimizing industrial production of commercially-relevant chemicals to studying disease patterns, be it within a set of human tissues or across animal model organisms. GEMs are complex and powerful tools. They comprise of thousands of reactions, mapping how metabolites are transformed through the activity of enzymes. Moreover, they aim to capture in vivo cellular behaviour under different phenotypic conditions by introducing the necessary abstractions for the entire metabolism.

Most often, systems biology requires the collection and integration of experimental data, and the same applies to GEMs. In the process of analysing experimental data, one recurring step is the visualisation of analysis results, regardless if the experiment is done in an academic or industrial setting.

Metabolic Atlas is dedicated to making GEMs easy to browse and analyse. Developed open-source by the Swedish ELIXIR node National Bioinformatics Infrastructure Sweden (NBIS) and freely available online at, the web portal integrates high-value open source GEMs developed by the Nielsen Lab at Chalmers University of Technology, now community-curated, and facilitates the access to the content of these models without any requirements. Moreover, it provides both automatically-generated and manually-curated maps, onto which omics data can be overlaid. Additionally, the manually-created maps have been the foundation of the collaboration with Protein Atlas, an ELIXIR Core Data Resource. Metabolic Atlas has also been showcased in the context of omics data integration, as part of the ELIXIR-SE Omics integration workshop.

The BioInnovation Institute Foundation (BII) is an international non-profit foundation supported by the Novo Nordisk Foundation, and it operates as an incubator to accelerate world-class life science innovations that drive the development of new solutions by early-stage life science start-ups for the benefit of people and society. A recent ELIXIR report on innovation in the life sciences highlights that “innovative life sciences projects require the essential use of open data, open-source software and common standards. Together, open resources allow industry, academia and the wider community to create novel services and products.” Acting as an interface between the academic community and industry, BII is aware of the importance of the open-source ecosystem as a startup need.

The Swedish ELIXIR node has an established systems biology dimension. In addition to the software development of Metabolic Atlas, NBIS provides expert bioinformatics support to the scientific community and occasionally to the industry. Last but not least, NBIS is also active in the recently established Systems Biology Community.

The goal of this project is to identify and retrospectively assess systems biology-themed activities geared towards industry with a focus on reproducibility, FAIRification and data management that can be carried out by NBIS. Specifically, the project will kick-off from how Metabolic Atlas can be leveraged by the industry and look further towards a long-term collaboration between BII and NBIS.


1 June 2022 to 31 May 2023

Nodes involved: