The digital lab

Keep your microorganism happy

Tuesday 14 Jun 22
|
by Morten Andersen

Contact

Ulrich Krühne
Assoc. Prof.
DTU Chemical Engineering
+45 45 25 29 60
A new Virtual Laboratory at DTU Chemical Engineering allows studying optimization of industrial bioprocesses.

Yeast, bacteria, and other microorganisms play the leading roles in a newly developed Virtual Laboratory at the Department. The lab has been developed with an educational goal with students as the primary target group.

“As chemical engineers, we have simulated traditional industrial processes for decades. Simulation of biological processes has been challenging, but since industry moves more and more into bioengineering, the value of being able to simulate bioprocesses has become apparent,” says PhD Researcher Simoneta Caño de las Heras, PROSYS, DTU Chemical Engineering. She has developed the virtual lab in her PhD project ‘Development of a Virtual Educational Bioprocess Plant’.

In its core, simulation of bioprocesses is not that different from other chemical engineering simulations, Simoneta Caño explains:

“For the most frequently used microorganisms in industry, we do have relatively reliable models. We know that if a given organism is subjected to a given temperature and level of nutrition etc., its growth can be projected mathematically. And when you can describe your system mathematically, you will also be able to optimize.”

However, some features do make simulation of bioprocesses extra challenging: “Microorganisms are alive. You may not necessarily see any dramatic events, but if the microorganisms are not “happy”, production will not be optimal.”

Developed by students for students

The lab is a virtual bioprocessing plant. A typical task might be to calculate the necessary volume and height of a bioreactor for a given purpose.

“We realized that our students simply need to have knowledge in this field. Optimization of bioprocesses does not only improve business cases in industry, but also contributes to making production more sustainable by minimizing the consumption of energy and other resources,” says Associate Professor Ulrich Krühne, supervising the project.

He adds that the primary goal is educational: “The problems to be solved in the virtual lab are all relevant in an industrial context, and possibly some companies may be able to benefit from using the lab, but first and foremost it is a tool for students—and made by students,” notes Ulrich Krühne.

Using the lab does require knowledge of bioprocesses, Simoneta Caño underlines: “Both bachelor and master students here at DTU will surely find the tool useful. The same goes for technicians operating bioprocessing facilities. Also, for instance a high school student wanting to explore the combination of biology and math as a possible future career path would be served well.”

Coding experience required

Further, users will need to have basic coding experience. This is a deliberate choice, according to Simoneta Caño: “Industrial bioprocessing is a field in rapid development. Therefore, we wanted to make it possible to enter new organisms, new processes, and new parameters.”

Coding is in PYTHON. Users may choose either easy, medium, or hard.

“When we tested the first version of the lab, some students complained about the tool being too easy, as they noted industry would expect them to have more advanced coding experience. Therefore, we decided to provide three different levels,” says Simoneta Caño, continuing: “Further, we have included coding exercises to encourage independent thinking. Some exercises have deliberate errors here and there, and the task is to find these errors. And sometimes the virtual laboratory will propose unfeasible scenarios while challenging the user to discover the problem. We want especially students to constantly consider what they are doing, not just have our software do all the work for them.”

The virtual lab is already being used by DTU bachelor students. It is available at www. biovl.com. Whether training in the virtual lab should be included formally in bachelor and/or master education is yet to be decided.

Contributes to sustainable solutions

Students will not be able to skip their hours in the physical labs just because they have access to a virtual one:

“The virtual lab cannot substitute for lab experiments. Instead, the virtual lab is a complementary tool which will help the students raise the quality of their experiments. In this way, the project is a part of the new trend of blending physical and virtual education,” notes Simoneta Caño.

She adds that considering the large societal benefits from better bioprocesses, it was decided that the lab should be openly accessible and free of charge: “This is a case of a public institution being able to contribute to more sustainable solutions. Further, we have created a tool that will not only benefit the students at DTU and other Danish universities. Just to take an example, South Africa is currently seeing a boom in bioprocessing. Bioprocessing innovators may not be able to pay for commercial simulators, especially not in developing countries. A tool like this, has a potential for making a difference in many places.”

New project will add artificial intelligence

In her project, Simoneta Caño has built the virtual lab all the way from the basic handwritten stoichiometric table on microbial growth over models to the graphic user interfaces. On the path to complete her PhD degree, she leaves DTU to work in biotech industry. Responsible for maintenance and further development of the virtual lab will be Fiammetta Caccavale who commences a new PhD project. Here, some artificial intelligence (AI) tools will be added. The AI will note the main interests of individual students, and thereby allow for personalized learning.

“To our knowledge, the lab could become the first biochemical engineering tool with built-in artificial intelligence,” says Simoneta Caño rounding off with a smile:

“During the last three years, I have become very connected to the virtual lab, but I am sure Fiammetta Caccavale will take good care of my “baby”!”.

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