Author: Anton Kravchenko, Senior Software Engineer, Earle A. Chiles Research Institute, Providence Cancer Institute
For many people, cancer research conjures images of scientists in lab coats, microscopes and test tubes. But the breakthroughs happening in cancer research also rely on coding, massive databases and computing infrastructure. That’s where the work of software engineering comes in.
At Earle A. Chiles Research Institute (EACRI), a division of Providence Cancer Institute, software engineers are integral to the multidisciplinary bioinformatics team. Although we’re not conducting laboratory experiments, we build the systems that make those experiments possible, reproducible and scalable. This allows our colleagues—immunologists, biologists and data scientists, including Brady Bernard, Ph.D., director of bioinformatics at Providence Cancer Institute and associate member in the Computational Immuno-oncology Laboratory at EACRI—to focus on advancing cancer research.
What is bioinformatics?
Bioinformatics employs software tools to analyze and manage complex biological data, such as genomic and transcriptomic datasets. In cancer research, these tools are critical for identifying mutations, understanding tumor evolution and evaluating potential therapeutic responses.
As software engineers, our responsibilities vary widely. One day, we might assist a researcher with debugging code used to analyze genetic variants. The next, we might create data workflows for a large-scale immunogenomics study or resolve issues related to open-source software integration. The information we gather and organize serves as a bridge between laboratory discoveries and clinical applications.
Although we work independently, our roles are also highly collaborative. We meet regularly with principal investigators to stay current on research goals because studies can shift quickly based on emerging needs. Sometimes a principal investigator needs data analysis for a study abstract or they may have technical issues that can impede progress in their research program.
Joe Slagel, manager of the Software Engineering team at Providence Cancer Institute, says we have to be both fluid and supportive colleagues and collaborators. “It requires us to use our software engineering skills in different capacities for various projects on a day-to-day basis,” he says. “I find it to be a very interesting place to work. The individuals we work with have a great deal of knowledge and expertise.”
AACR Project GENIE
One of our most exciting collaborations is with the American Association for Cancer Research (AACR) Project GENIE, an international, multi-institutional effort to build a large, shared genomic data set that can support clinical decision-making and research across cancer types. Participating in the GENIE consortium is important and exciting work, as it contributes to better cancer treatments and care worldwide.
Our software engineering team supports Project GENIE by managing the extraction, transformation, validation and uploading of clinicogenomic data to the GENIE consortium. This effort requires collaboration across Providence teams to maintain high data quality for consumers of GENIE datasets. We continue to expand our contributions in size and breadth each year, ranking as one of the largest contributors across participating cancer centers.
EACRI Data Lake
Recently, we have focused on developing a Data Lake, a centralized source to organize research data and analysis results for later inquiry. This project is built using cloud computing technologies, allowing us to streamline data governance and enhance collaboration across Providence teams. The EACRI Data Lake facilitates retrospective analysis and enhances study design for principal investigators at EACRI. Our role is to create and maintain infrastructure and data workflows to integrate rapidly evolving data sources. Without this system, reviewing large quantities of past data would be significantly more challenging.
Why it matters
Ultimately, our role is to enable scientific research. We are not subject-matter experts in cancer biology, but we have expertise in building systems that can ease the way for cancer researchers we support. It is rewarding work, especially when we see how the right software or data solution can accelerate discovery or improve the long-term health and well-being of cancer patients.
Find out more about the Computational Immuno-Oncology Lab at Earle A. Chiles Research Institute.
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