For too long, biotech innovators have viewed biological systems as inherently messy, unpredictable, and full of “black box” mysteries. But what if, armed with the latest digital tools, AI, and cross-disciplinary thinking, you could transform bioprocessing from a series of trial-and-error experiments to a streamlined, proactive design process?
This is the second part of a conversation between David Brühlmann and Carmen Jungo Rhême, a professor at the University of Applied Sciences in Fribourg, Switzerland, and director of the Biofactory Competence Center (BCC). They discuss how digital tools, real-time data modeling, and artificial intelligence are transforming bioprocess development—and shifting our perspective from viewing biology as unpredictable to seeing it as something designable and controllable.
Key Topics Discussed
- How the Biofactory Competence Center bridges academia and industry through applied research, technology transfer, and hands-on bioprocess innovation.
- The collaborative framework guiding partnerships with biotech companies—from feasibility studies to full-scale process transfer and implementation.
- Why small-scale bioreactors and digital modeling are redefining process development, enabling accurate simulation of industrial-scale bioprocesses.
- How the BCC’s training programs prepare students and professionals for modern biomanufacturing, combining GMP foundations with technical problem-solving.
- The emerging skillset for next-generation biotechnologists, including data interpretation, adaptability to digital tools, and systems-level thinking.
- Inside the BCC’s current projects tackling antimicrobial resistance, sustainable food production, and data-enhanced process optimization.
- How digital twins, AI, and real-time modeling are transforming biology from an unpredictable system into a designable, controllable discipline.
- The mindset shift needed in biotechnology—from reactive experimentation to proactive, design-driven innovation supported by digital transformation.
Episode Highlights
- Shifting the mindset from “biology is messy” to “biology is designable,” and how this change is shaping the future of biotech [00:00:00]
- The mission and collaborative approach of the Biofactory Competence Center, including research and training activities [00:03:13]
- Structuring projects with startups and large companies—feasibility studies, process development, analytics, and scale-up to GMP [00:04:40]
- The role of digital modeling and data-driven decision-making in direct scale-up from lab to production [00:07:00]
- Practical and technical skills training, including programs for GMP operators and advanced process engineers [00:08:42]
- The three most valuable skills for the biotech workforce over the next five years: data management, digital adaptability, and systems thinking [00:10:54]
- Ongoing work in antimicrobial resistance and sustainable food production in Switzerland, including collaborations with innovative startups [00:13:56]
- A case study on digital transformation: leveraging AI and digital twins for accelerated bioprocess development [00:17:30]
- Key takeaway: mastering complexity in bioprocessing with the right mindset, tools, and training [00:19:54]
- Ways for listeners to connect with Dr. Jungo and explore opportunities at the BCC [00:20:49]
In Their Words
With the tools we have today—particularly digital tools, real-time data modeling, and AI—we can understand and control biology in ways that were unimaginable just a few years ago. If we shift our mindset from “biology is messy” to “biology is designable,” it changes everything. I think it opens the door to more robust and faster process development, leading to quicker innovation and truly sustainable solutions. This mindset shift—from reactive to proactive, or from trial-and-error to design-and-control—is what will define the future of the biotech industry.
Episode Transcript: From Biology Is Messy to Designable: The Smart Bioprocessing Transformation - Part 2
David Brühlmann [00:00:51]:
Welcome back to part two with Carmen Jungo Rhême, who is a professor at the University of Applied Sciences in Fribourg, Switzerland, and director of the Biofactory Competence Center.
If part one inspired you about fighting superbugs and sustainable food production, you’ll love this deep dive into the Biofactory Competence Center’s revolutionary approach.
We’re exploring how their non-classified cleanrooms seamlessly transfer to GMP facilities, their practical idea-to-scalable-process methodology, and the critical skill gaps Carmen has discovered while training both newcomers and industry veterans.
Ready to discover what makes bioprocess development truly scalable? Let’s dive in.
Now, let’s talk more specifically about what you’re doing at the Biofactory Competence Center. You’re a professor at the University of Applied Sciences in Fribourg and also leading the Biofactory Competence Center. We’ve mentioned that term several times already. Tell us a bit more — what is this center all about? What’s your mission, and what specific challenges and needs are you addressing?
Carmen Jungo Rhême [00:03:13]:
At the Biofactory Competence Center, our main goal is to work in collaboration with industrial and academic partners on applied research projects.
Universities typically focus on fundamental research, while universities of applied sciences, like ours, focus more on applied research. We collaborate with startups as well as larger companies — mainly in biotechnology, including the pharma and food industries.
On top of that, we also offer training for our students — practical training and theory in bioprocess engineering — and for professionals from industry, typically in upstream and downstream processing, as well as other skills such as aseptic techniques.
David Brühlmann [00:04:15]:
Let’s assume I’m the CEO of a startup company with a new technology or idea, and I need a development partner like your center. How does this process work? We come to you and say, “Hey, we have this amazing idea to solve antimicrobial resistance.” What happens next?
Carmen Jungo Rhême [00:04:40]:
Each project is different, but we always follow a structured approach. When a biotech company — large or small — comes to us with an idea, we start by listening and understanding their concept, goals, and challenges.
From there, we typically guide them through four key phases:
- Feasibility Study / Concept Design: We assess the scientific and technical viability, identify risks, evaluate technology readiness, and define critical quality attributes.
- Process Development: Once the concept and goals are clear, we co-develop a robust upstream or downstream process (or focus on one step). For recombinant proteins, this may include selecting the expression system, optimizing media and process variables, and ensuring scalability and GMP implementation.
- Analytical and Quality Strategy: Done in parallel, we tailor an analytical toolbox to monitor product quality and process performance — essential for future GMP manufacturing.
- Scale-up / Technology Transfer: Finally, we support the scale-up or technology transfer to a manufacturing facility.
This is the general framework we follow.
David Brühlmann [00:07:00]:
Speaking of scale-up — when transferring to another partner, CDMO, or in-house facility — what are the typical scales you work at in your facility, and at what point do you transfer?
Carmen Jungo Rhême [00:07:20]:
We typically work with 5-liter bioreactors, which can mimic very well a 15,000-liter system. Most of our development studies are performed at 5-liter scale. We also have 50-liter bioreactors, but we often focus on the 5-liter scale because scale-up can be done directly to much larger systems — 1,000 or even 15,000 liters. This is quite common in the industry. You often lose too much time moving through intermediate pilot scales before final manufacturing.
David Brühlmann [00:08:00]:
Exactly — especially with digital tools and modeling, if your small-scale system is well-characterized, you should have everything you need to scale directly and succeed.
Carmen Jungo Rhême [00:08:14]:
Yes, definitely.
David Brühlmann [00:08:16]:
At the Biofactory Competence Center, you both co-develop with companies and train people for GMP or lab work. Tell us more about your training programs and the skill gaps you’re addressing.
Carmen Jungo Rhême [00:08:42]:
We offer operator training for the pharmaceutical industry. Over the last ten years, many facilities were built in Switzerland, and the industry had to hire a large number of operators. That’s why this training was created — to prepare competent people for GMP operations. It’s a five-week program covering GMP documentation, lab practices, pH and conductivity measurement, gowning, and more. For more advanced professionals, we also offer three-day trainings — one in upstream processing and one in downstream processing.
David Brühlmann [00:09:47]:
And those advanced trainings — are they GMP-focused or more technical?
Carmen Jungo Rhême [00:09:58]:
They’re more technical and scientific, not focused on GMP. For example, in the upstream course, we cover mass balance, calculating specific growth rates and doubling times, and determining feed rates for fed-batch cultures. So yes, more technical than regulatory.
David Brühlmann [00:10:25]:
You train university students and industry professionals, while the industry itself is changing rapidly — robotics, AI, digitalization. What do you think will be the top three skills that matter most in five years?
Carmen Jungo Rhême [00:10:54]:
That’s a good question. Many skills are important, but I’d highlight three:
- Data Management: Not just collecting data, but contextualizing, interpreting, and making decisions based on it.
- Adaptability with Digital Tools: Not necessarily coding, but being comfortable with digital platforms, automation, AI, and modeling tools — all now part of daily lab and manufacturing life.
- Systems Thinking: Understanding how different parts of a process or ecosystem interact — beyond just process parameters. That includes raw materials, suppliers, and environmental factors.
This broader view is essential.
David Brühlmann [00:12:28]:
Absolutely. Systems thinking is often overlooked, yet it’s fundamental. In a connected world, being able to “connect the dots,” as Steve Jobs would say, helps professionals stand out and even turn their data into valuable assets.
Carmen Jungo Rhême [00:13:11]:
Exactly. Data is key — and systems thinking helps you use not only process data but environmental data, too.
David Brühlmann [00:13:25]:
You’ve been leading the Biofactory Competence Center for about a year and a half. What’s your vision for the next few years?
Carmen Jungo Rhême [00:13:56]:
In the coming years, I want to continue working on antimicrobial resistance — it’s a major global challenge. We’re collaborating with a Swiss startup, Micreos, based in Baden, where we express and purify endolysins to fight Staphylococcus aureus. I’m also passionate about sustainable food production, especially in Switzerland. Using waste products efficiently and combining them with digital tools to maximize data and outcomes is one of our goals.
And, of course, continuing to deliver impactful training for students and professionals — and learning from them in return — helps us keep improving.
David Brühlmann [00:15:30]:
Switzerland has always adapted quickly — to environmental, industrial, and now technological changes. What kind of mindset shift do you think we need as scientists moving forward?
Carmen Jungo Rhême [00:16:08]:
We need to stop seeing biology as unpredictable. For too long, biological systems have been treated as black boxes — mysterious and variable. But with digital tools, real-time data modeling, and AI, we can now understand and control biology in unprecedented ways. If we shift our mindset from “biology is messy” to “biology is designable,” it changes everything — enabling more robust, faster, and more sustainable processes.
This shift, from reactive to proactive and from trial and error to design and control, will define the future of the biotech industry.
David Brühlmann [00:17:21]:
Before we wrap up, what important topic haven’t I asked about that you’d like to share with our biotech community?
Carmen Jungo Rhême [00:17:30]:
We also have projects in digital transformation.
For example, we’re collaborating with DataHow and Beckman Coulter on a project funded by Innosuisse’s Innovation Booster. The goal is to demonstrate how digital technology and AI are transforming biotech.
The project focuses on optimizing green fluorescent protein (GFP) production in E. coli fed-batch cultures. We run design-of-experiment studies using Beckman Coulter’s BioLector XT micro-bioreactor system — a high-throughput platform that allows many experiments in parallel.
All process data is collected and used by DataHow to build a digital twin — a hybrid model to identify optimal process conditions quickly. It’s both a research and educational project: our students learn to use digital twin tools so they can apply them in industry.
David Brühlmann [00:19:40]:
Fantastic — I love this project. With everything we’ve discussed today, what’s your 22nd takeaway?
Carmen Jungo Rhême [00:19:54]:
Bioprocessing today isn’t just about managing complexity — it’s about mastering it. With the right mindset, tools, and training, we can turn biological variability into predictable, scalable, and sustainable solutions. Whether it’s fighting antimicrobial resistance, transforming food systems, or embracing digitalization — the future of biotech is about integrating the right tools for smarter bioprocessing.
David Brühlmann [00:20:38]:
Thank you so much, Carmen, for sharing your passion and expertise. Where can people connect with you?
Carmen Jungo Rhême [00:20:49]:
People can connect with me on LinkedIn or through the Biofactory Competence Center website — there’s an email address for inquiries or collaborations.
David Brühlmann [00:21:08]:
That’s great. I’ll leave all the information in the show notes. Thank you once again, Carmen, for being on the show today.
Carmen Jungo Rhême [00:21:31]:
Thank you very much, David. It was a pleasure.
David Brühlmann [00:21:34]:
Fantastic insights from Carmen Jungo Rhême on the future of bioprocess development and training — from seamless GMP transfers to essential skills for the next five years.
Remember, scaling doesn’t have to be overwhelming. If you need guidance on your process or technology development journey, schedule a free consultation at Brühlmann Consulting.
Thank you for tuning in — please leave a review and I’ll see you next time. All right, Smart Scientists — that’s all for today on the Smart Biotech Scientist Podcast. Thank you for joining us on your journey to bioprocess mastery. For more tips, visit smartbiotechscientist.com and stay tuned for more inspiring biotech insights. Until next time — let’s continue to smarten up biotech.
Disclaimer: This transcript was generated with the assistance of artificial intelligence. While efforts have been made to ensure accuracy, it may contain errors, omissions, or misinterpretations. The text has been lightly edited and optimized for readability and flow. Please do not rely on it as a verbatim record.
Next Step
Book a free consultation to help you get started on any questions you may have about bioprocess development: https://bruehlmann-consulting.com/call
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About Carmen Jungo Rhême
Carmen Jungo Rhême is full professor at the Haute Ecole d’Ingénierie et d’Architecture de Fribourg (HEIA-FR) and Director of the Biofactory Competence Center (BCC). She has extensive experience (17 years) in the pharmaceutical industry with a proven track record in several biopharmaceutical companies manufacturing therapeutic recombinant proteins (Lonza, Merck Serono, UCB Farchim and CSL Behring).
She specialized in bioprocess development, both in cell culture and in purification of proteins, scale-up, and technology transfer of marked products. Since her start at HEIA-FR in November 2023, C. Jungo Rhême has initiated several research projects in the field of antimicrobial resistance, one of them in the field of antimicrobial resistance, sustainable food production, and digitalization of bioprocesses.
Connect with Carmen Jungo Rhême on LinkedIn.
David Brühlmann is a strategic advisor who helps C-level biotech leaders reduce development and manufacturing costs to make life-saving therapies accessible to more patients worldwide.
He is also a biotech technology innovation coach, technology transfer leader, and host of the Smart Biotech Scientist podcast—the go-to podcast for biotech scientists who want to master biopharma CMC development and biomanufacturing.
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