Faces of Innovation
Meet Scott Newberry: Director of the HudsonAlpha Strategic Software Group
By: Jazmine Robinson
The fields of AI and software development are exploding, constantly pushing the boundaries of what’s possible. It can feel like a wholly new frontier, but many dedicated professionals have been instrumental in its journey. For this “Faces of Innovation” feature, we sat down with Scott Newberry, Director of the HudsonAlpha Strategic Software Group. Join us as we explore his journey and insights from years of experience in this dynamic and rapidly expanding industry.
Jazmine Robinson: I’m familiar with what an IT department does, but strategic software was a new term for me when I came to HudsonAlpha. Can you explain what you do in the strategic software group?
Scott Newberry: We write applications that mainly support research. We’ve done a little work with Educational Outreach, but primarily we write things such as laboratory information management systems used by researchers. One of our big applications is called CODICEM or Codi for short, which is used to identify rare variants that may cause genetic disease.
Codi has been under development for the past 8 years or so by my group. It’s designed to annotate, filter, and curate variants from whole genomes to aid analysts in finding the ones that give rise to rare disease. We are currently expanding Codi to be able to be used with data from the new long-read sequencing done on the PacBio Revio.
Jazmine: Interesting. Do you have a background in science?
Scott: My background before coming to HudsonAlpha was mostly computer science/software. I’m a career software developer. I have a software engineering degree and an applied math degree from Auburn. I began my career in defense, then came here, where I suppose I can be considered more of a bioinformatician. I’ve been here for 15 years, and I’ve learned any and all of the genetics, genomics, and life science information that I know on the job.
Jazmine: What would you say has been a pivotal point in your career that has led you to this moment?
Scott: There weren’t many biotech jobs here in Huntsville, so my wife (Research Associate Kim Newberry of the Myers Lab) and I lived in D.C. for work. My dad sent us the newspaper announcement of HudsonAlpha’s opening in 2008 and we decided to move. Fast forward a little bit, Kim started working here, and I transferred from Lockheed’s facility in D.C. to their Huntsville location.
I would visit Kim in the lab, not considering that a place like HudsonAlpha would need career software developers. But bioinformatics was burgeoning, and as I talked to people in the lab, I realized that my skill set could be used here. This work seemed a lot more appealing to me than the work I had done previously, from the nonprofit aspect, the genomics aspect, the research aspect – all of it. When I made the decision to come to HudsonAlpha, the career trajectory I would have followed is completely different than if I had remained in defense. The decision to come here is the pivotal defining moment.
Jazmine: So, thinking of that pivot from defense to HudsonAlpha, what would you say has been the most exciting part of that career shift?
Scott: One of the most exciting things about my job is that every day I am surrounded by and have the opportunity to learn from people who are smarter than I am, people who are very, very passionate about what they do and very, very good at doing it. I know it’s the vision, but we truly are using genomics to improve life. We get to say it, and we get to live it. This is what keeps me coming back through the doors every day.
I know it’s the vision, but we truly are using genomics to improve life. We get to say it, and we get to live it. This is what keeps me coming back through the doors every day.
Jazmine: I know exactly what you mean! Knowing that we play a role in bringing the vision to fruition is so… rewarding. People don’t necessarily think about the software behind the science when we think about the ways we are changing the world, but it’s integral to the work being done.
Scott: This is really important, especially in genomics and sequencing. Behind the scenes, there’s a major analytical component, and it’s all driven by software. As sequencing has become more affordable, the analytics side has grown tremendously and now plays a huge role in the field.
Jazmine: Is there anything new on the horizon that you could potentially share with us?
Scott: My group is exploring how to integrate AI with various workflows throughout the Institute. We have already integrated AI tools into one of our applications, PODS, which is an experiment management system for one of the groups doing work with plants. We’ve also released some AI-powered cluster tools that help users optimize their resource requests. We are looking forward to doing more of this work as well as integrating long read technology into Codi.
Jazmine: I am fascinated by the advancements in AI and how we’re able to utilize that in our research here. Have we been doing this for a while?
Scott: These days, when you say AI, people mean something like ChatGPT, Large Language Models, or LLMs, which we have not been using specifically for research until rather recently. Most of its use right now has consisted of asking questions, and it helps to either write code or search the internet on your behalf. Now, there are more ways that we can integrate it into more sophisticated models, specifically built around genomics that we are aware of. We’ve talked about it a little bit and are excited about the possibilities.
Jazmine: Do you see the future of software being more AI-focused?
Scott: I think software development, as well as a few other professions, are going to undergo a pretty big shift with the advancement of AI technology. I see it as the equivalent of having a really smart intern, where it’s right 80% of the time, but then you need to go find the 20% where it’s wrong. I think a software developer’s role in the future is going to consist less of writing new code and more of telling an AI agent what to do: analyzing it, then editing, fixing it, and making it work better within the application that you’re writing.
Jazmine: Has this new shift been surprising for you, based on your career background?
Scott: I’m surprised at how fast it’s advanced. If you had asked me a year ago, ‘Could AI do a particular project?’ I would have said, eventually, but I wouldn’t have expected it to happen within the next six months.
Jazmine: So, the advances in technology are moving even faster than those of you in the software field expected?
Scott: Absolutely. You can prompt it to make a plan for how you would tackle a project. It’ll search your code base, make a plan, and then ask, ‘Hey, do you want me to go do this?’ And they’ll do step one, step two, step three, all separately. Software development is well-suited to AI because programming languages are well-structured. These are things that LLMs and AI understand really well. But this, I think, is going to be applied to other fields as well, right where it can come back with some insights, and then your role is to go through and decide how well it answered your question.
Jazmine: With so much advancement in sequencing technology, the addition of AI, and just an overall shift in the field, what would you say is one of the more challenging parts of your role?
Scott: One of the biggest challenges for any software team is developing tools to help people track their data and what they can do with it. For any one person, that’s a tractable problem, but you multiply that by 50 people who are generating and downloading data, and it can be challenging. We work very closely with IT to develop tools to help manage the data and storage. We have a handle on data growth today that is better than ever, and that’s largely due to how well we work with IT, the researchers working well with us, and entrusting us to provide them with the tools that we can use to help them manage their data.
Jazmine: What advice would you give to aspiring young professionals who are looking for a career in software development?
Scott: Learn how to use AI! I say that, but be intentional about it. If you’re still in school, try not to rely on it for assignments. Focus on really learning the material, because that foundation matters. For those early to mid-career, I’d really encourage you to put in the time to understand the fundamentals of AI. Knowing how to use these tools is becoming a must in the field, and staying current is going to be key to staying competitive.
