Designing software for microbiologists and geneticists

Allen Clarke, a Computer Science and Mathematics double major, has been sharpening his software development abilities at NAU’s Pathogen and Microbiome Institute (PMI). He is leveraging his programming expertise to create tools that help PMI researchers complete their cutting-edge work on gene sequencing.

“An analogy I’ve heard a lot is they’re building the plane while it’s taking off,” he said. “The researchers kind of know where they’re going, but they don’t yet have all the pieces they need to get there.”

Clarke is helping to put those pieces together. His aspiration is to become a software developer, a profession that connects his interests in web development and database management.

Clarke’s current project at PMI focuses heavily on both interests. He is expanding his knowledge of database management by ensuring the security of researchers’ data; he is also preparing PMI’s Google Sheets database to accommodate potentially extensive data sets. His software development skills are in high demand. The work is never truly done, as researchers routinely introduce new elements to the system.

Clarke explained PMI researchers use 10x gene sequencing on pathogens. Although in the past they may have identified only one feature barcode to use when sequencing data, many now identify four feature barcodes because of advanced DNA sequencing, and databases need to accommodate the added complexity. The use of additional feature barcodes enables geneticists to get longer DNA reads out of sequencers designed to handle shorter DNA reads.

Because of this project, Clarke has also been exposed to three different programming languages—essential to his dream career as a software developer. “I’ve been doing a lot of back-end work in one language, Go,” he said. “I also have been doing some front-end work with Google Sheets in JavaScript and developed some websites in HTML.”

When he began working at PMI, Clarke felt overwhelmed by everything he needed to learn and concerned that he wasn’t up to the task of working at a research facility. Public speaking was also an uncomfortable prospect. He credits PMI associate director Dawn Birdsell’s mentorship for helping him to overcome these challenges. Birdsell routinely helps student researchers develop presentations for the university’s Undergraduate Symposium. At last year’s event, Clarke had advanced so much he earned second place in the competition’s research category.

Clarke is impressed with the opportunities he’s been given at NAU.

“The fact that there are so many undergrad research opportunities relative to the number of undergraduates here blows my mind,” he said. “I’m thankful I can look back at the work I completed at PMI and say I contributed to something meaningful.”