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Chemist on the Trail of Algorithms

Merging Science, Programming AND DRUG DISCOVERY

Karol Bubała - Scientific Software Developer, expert in drug discovery process
Karol Bubała, Scientific Software Developer at Sigma IT Poland

Discover the fascinating journey of merging science, programming and its transformative impact on the drug discovery world. Meet Karol, a chemical engineering graduate who helps to change how scientists work. Gone are the days of manual processes heavily reliant on vast knowledge, intuition, and exceptional memory. Thanks to Karol’s expertise, scientists can now harness the power of software to streamline their work and achieve remarkable breakthroughs. He describes himself as a Java developer by heart, a Python developer by necessity, and a cheminformatician by accident.

SIGMA IT POLAND: What caught my attention in your story is that, as a chemical engineering graduate, you one day found yourself more interested in programming than conducting experiments. Before I ask how that happened, please briefly explain your role at Sigma IT Poland.

Karol Bubała: I work for a client in the biotech industry, specializing in drug discovery and design. My role involves developing a platform that assists in this process.

Professional journey

Could you share a bit about your professional journey? I heard you went through an interesting career change.

After finishing high school, I pursued studies in chemical engineering. It’s a field where we take the ideas developed by chemists and figure out how to apply them in practical industries. For example, while a chemist performs experiments in a flask to create chemical compounds, a chemical engineer asks, “Okay, the flask reaction works, but how can we scale it up to produce 30 tons per day for industrial purposes?”

Impressive! When did your interest in computer science arise?

Later, I pursued a doctoral degree in chemical engineering, and within that program, I began focusing more on mathematical modeling of processes. This involved writing scripts, collecting and processing data, and calculating model parameters. Eventually, I realized this aspect brought me the most joy during my doctoral studies.

cheminformatics industry

How did you enter the cheminformatics industry?

A friend of mine forwarded me a job posting seeking a programmer with a background in chemistry. I realized that I might not fit the typical chemist profile, but I had more knowledge of chemistry than the average programmer. So, I applied for the position and got selected for a project with a leading scientific and technological company operating in the healthcare and life science sectors.

What was unique about that project?

At that time, I was working on a tool to assist in retrosynthesis. Let’s say we have a naturally derived substance with excellent cancer treatment properties, but it can only be obtained at very deep depths. That’s where retrosynthesis comes in, helping to recreate the same compound in the laboratory. We look back at the reactions that can produce the desired compound.

solving complex puzzles

It sounds like solving complex puzzles. What challenges did you have to face in this project?

The algorithm generates a set of reactions that can produce the desired compound, but the substrates of such reaction also have no known synthetic pathway. We systematically expand the range of possibilities until we discover a viable pathway, starting with readily available substances from chemical suppliers. The number of combinations grows rapidly, starting with a couple of candidates after the first expansion and reaching thousands in just a few steps. This task used to be done manually for years! It demands extensive knowledge, intuition, and the ability to remember numerous reaction mechanisms and patterns. I contributed to developing an algorithm that simplifies the search and assessment of potential pathways.

I hear you have a talent for translating complex concepts into understandable language for non-experts. That must be a valuable skill at everyday work.

Absolutely! First, I would listen to scientists, try to comprehend their objectives, and understand the purpose of the tools they are developing. Then, I would go to the programmers and say, “Okay, this is the goal; this is what we want to accomplish. We need to pay attention to these aspects and outcomes.”

Collaboration BETWEEN scientists and programmers IN DRUG DISCOVERY

How do you see the collaboration between representatives of these two worlds – scientists and programmers?

Both worlds have something valuable to offer. Programmers know how to create stable, maintainable, and scalable solutions. However, they often need domain-specific expertise. On the other hand, scientists develop solutions that address specific problems, but they typically lack knowledge about software development best practices. When a large company acquires such software and intends to turn it into a product, it must reconcile these two worlds and find common ground. I was in a great position to coordinate these two realms and facilitate effective communication.

Can you tell me about the next project where you further developed as a programmer?

Next, I worked on an electronic laboratory notebook with additional features. The goal was to record results and provide an environment for data processing, visualization, and the ability to execute scripts for automated data analysis. These systems can be quite complex.

What was unique about this project?

The client aimed to build a team of programmers with a background in the sciences. I assisted in the development of the platform and had the opportunity to gain a more in-depth understanding of the biotech field, particularly around environmental monitoring.

What does environmental monitoring specifically involve?

Environmental monitoring focuses on ensuring cleanliness and maintaining proper procedures in biotechnological laboratories where bacterial cultures, molds, and other substances are present. I worked on developing an application responsible for scheduling and controlling the cleanliness requirements of these environments.

What other experiences in the biotech field did you manage to gain?

After that, I transitioned to another project focused on clinical operations, which involved managing and scheduling clinical trials. This project aimed to define, plan, and control the execution of entire clinical trials. It shifted more toward development rather than design, but I remained within the realm of drug discovery. There aren’t many people who have both programming skills and chemical backgrounds. The projects in this area are truly remarkable!

Satisfaction at DRUG DISCOVERY work

What gives you the greatest satisfaction in your work?

I’m not just developing another application that generates millions for a corporation, but I’m contributing to potentially saving someone’s life or improving their quality of life. That is truly incredible. I’m doing something meaningful and valuable in my everyday work.

What attracted you to the position you currently hold at Sigma IT Poland?

The client we work for is one of the most advanced companies when it comes to utilizing computer methods in drug design. They are among the top players globally regarding their forward-thinking approach and dedication to this field. Joining Sigma IT Poland was a perfect match for me. I find fulfillment in my role here. I learn something new almost every day, and at the same time, the experience I gained from my previous four years of work on various projects also helps me deliver value to the client.

Could you please share something you enjoy doing in your spare time?

Outside of work, my main interests revolve around my children, my primary focus outside my profession, especially since I recently became a father for the second time. I also enjoy hiking in the mountains, and some time ago, my wife and I started conquering the Polish Mountain Crown. Now, we plan to start again with our sons. I also love playing various board games, card games, computer games, and classic RPGs.

Karol, thank you very much for the interview, and I wish you many exciting challenges in your career!

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