Using big “bio-data” to design better cell factories

Friday 01 Apr 16
by Anne Lykke

Facts about DD-DeCaf

  • DD-DeCaF (Bioinformatics Services for Data-Driven Design of Cell Factories and Communities) brings together leading academic partners from five European universities with five innovative European companies to address the challenge of building a comprehensive design tool.
  • The DD-DeCaF project is a collaboration between the Technical University of Denmark, Chalmers University (Sweden), European Molecular Biology Laboratory, University of Minho (Portugal), Ecole Polytechnique Federale de Lausanne (Switzerland), SilicoLife Lda (Portugal), Genialis d.o.o. (Slovenia), Biobyte solutions GmbH (Germany), Biosyntia A/S (Denmark) and DSM N.V. (the Netherlands).
  • The academic partners will develop cutting edge methods for using large scale data to design cell factories and communities for biotechnological applications.
  • The project was launched 1st of March 2016 and runs over a 4-year period.
  • The grant was given as part of a call from EU within the Horizon2020 program ‘New Bioinformatics approaches in service of Biotechnology’.

The EU has granted 6.3 million Euros to the project DD-DeCaF, coordinated by the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark. The objective is to develop a computer tool that will allow biotech companies to design and engineer cell factories faster than is currently possible today. The tool will accelerate the production of sustainable bio-chemicals and lay the groundwork for design of healthier foodstuff.

Today, many valuable molecules used in consumer goods, for example plastic diapers, cosmetics and food can be produced by cell factories – genetically engineered microbes such as baker’s yeast and E. coli.

"The biotech industry is in great need of a computational design tool that allows them to simulate how a cell will behave if you engineer it in a certain way"
project coordinator of DD-DeCaF, Professor Markus Herrgard

But engineering microbes to produce large amounts of a given bio-chemical is very complicated, time consuming and expensive.

Data called omics (for example genomics) allows life scientists to survey the cell’s molecular components and molecular pathways. Unfortunately, biotech industry has not yet been equipped with tools that allow them to make effective use of this data.

The scope of the DD-DeCaF project is therefore to develop an easy to use web application that collects all this data and evaluates the consequences of specific changes to the cell's genome.

“The biotech industry is in great need of a computational design tool that allows them to simulate how a cell will behave if you engineer it in a certain way – just as engineers design and test buildings before they build them,” says project coordinator of DD-DeCaF, Professor Markus Herrgard from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at the Technical University of Denmark.

Need for an intuitive user interface

The web platform will have an intuitive and user friendly interface that will enable exploratory data analysis through interactive and interconnected visualizations.

“The idea is to build a tool the industry can easily use and adapt to their specific needs. Today, we have so much data and knowledge about the biological pathways operating inside these industrial microorganisms. This enables us to use mathematical models to simulate the effects of genetic modifications and thus facilitate a more rational approach to the design of cell factories.” says Scientist Nikolaus Sonnenschein from the Novo Nordisk Foundation Center for Biosustainability.

The tool will therefore reduce the costs of developing cell factories, making them able to compete with currently used unsustainable petrochemical processes. 

The tool will be tested by the industry

Three small and medium sized bioinformatics companies – Biobyte in Germany, SilicoLife in Portugal and Genialis in Slovenia – will be involved in the development of the software tools and intuitive visualizations of biological networks that can be used by non-experts.

Simultaneously, two industrial biotech partners – the DTU spin-off company Biosyntia and the Dutch multinational company DSM with more than 20,000 employees – will utilize the tool in two real-world cell factory projects and thus continuously evaluate the tool’s usability from two very different user perspectives.

“We will have a lot of valuable feedback from the industry telling us what works and what applications are missing. In this way, we will continuously improve and tailor the tool to the needs of the industry,” says Nikolaus Sonnenschein.

Biosyntia is developing bacterial strains and fermentation processes that allow sustainable, biological production of a number of B-vitamins for food, feed, and pharmaceuticals.

“With this tool, analysis of complex biological data will be easier than ever before and become directly accessible to bench-scientists. The platform will be of great value to strain engineering companies like Biosyntia and ultimately help accelerate the development of cell factories with benefits for health and environment” says Hans Genee, co-founder of Biosyntia.  

DD-DeCaF can lead to healthier food

DD-DeCaF also aims at exploring interactions between cell communities and obtaining novel data about the interplay between microbes. For example, the human gut consists of many different cell types that interact and compete with each other.

If some cell types begin to dominate the gut, or if communities fight each other, this may lead to diseases. Being able to describe these cell interactions computationally, the industry will eventually be able to develop food and pharmaceutical compounds with beneficial implications on the gut.

Find out more about the project at


Professor Markus Herrgard, E-mail:

Researcher Nikolaus Sonnenschein, E-mail:

Co-Founder and CSO at Biosynthia Hans Genee, E-mail:


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