Computer Aided Design of Cell Factories

Computer power used in design of cells for biological production

Wednesday 25 Nov 20


Nikolaus Sonnenschein
Associate Professor
DTU Bioengineering

Computer Aided Design of Cell Factories

The course Computer Aided Design of Cell Factories must give students a basic understanding of the interaction between the many different reactions between the cells in cell factories, and especially how the flow in the different biosynthetic pathways is regulated. Particular focus will be on biosynthetic pathways that may lead to industrially relevant products such as primary metabolites, antimicrobial agents, industrial enzymes, and pharmaceutical proteins.
A key aspect of the course is cell factory modelling to help identify optimal strategies for introducing targeted genetic changes in microorganisms to produce better production strains. Analysis of the interplay between different cellular responses is another key element of the course, and tools for characterizing strains at a systemic level as well as design will be described. Based on a number of different modelling tools, students will learn to model and design cell factories primarily using programming.
DTU offers new courses in handling large data sets using programming and artificial intelligence, AI.

A course in Computer Aided Design of Cell Factories at DTU will strengthen the students’ competencies in programming and computer simulations. The course focus on knowledge and methods for utilizing data in biology comes after increasing demand from biotech companies.

“There is a recognition in the industry that basic programming with the code language such as Python is important. The companies are looking for graduates with those competencies, and they have a desire to train their employees in the field, so that the workflows in designing cell factories can be digitized and become data-driven,” says Associate Professor Nikolaus Sonnenschein, who teaches the new course.

Computer Aided Design of Cell Factories is offered for the first time in the 2020 autumn semester under the auspices of DTU Bioengineering and in 2021, the course is expected to be offered as continuing education through DTU Learn for Life. Nikolaus Sonnenschein has previously taught a version of the course at DTU Biosustain.

Less impact on the environment

The first class of 75 students at Computer Aided Design of Cell Factories are currently doing the course at DTU Bioengineering, where they are taught theory and fundamental skills and the data models and programming tools on which the course is based. The course provides insight into examples of designed cell factories that have led to new products, improved productivity, better raw material utilization, and less impact on the environment.

Nikolaus Sonnenschein explains that the programming data are based on known observations and data that previous researchers have mapped in terms of biochemical reactions in the various organisms. Data from new production cells can be derived from genetic engineering with CRISPR technology, which makes it possible to leverage the ability of proteins to remove or insert specific DNA sequences into new organisms. These data are transferred to data models, where they are included in calculations and simulation of the cell properties.

Computational modelling

In biological research it has become almost trivial to remove or add a gene, or make more extensive changes, which previously could take researchers years to document and analyse.

“Digitization of research can create or simulate the same results in no time, and the focus has shifted. Genetic engineering is no longer the bottleneck and computational modelling can help us choose what modifications to do,” explains Nikolaus Sonnenschein.

Computer Aided Design of Cell Factories will be anchored in a Data Science Core Facility at DTU Bioengineering, which is currently under development and will support researchers and students in their work with handling large amounts of data that can be automated and processed in more advanced models.

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