#WhyIScience Q&A: A software engineer develops computational tools for psychiatric and brain research

Khalid Shakir talks about his work analyzing large single-cell datasets, his excitement around AI, and the importance of mentorship and community in science. 

Khalid Shakir is a principal software engineer in the McCarroll Lab.
Credit: Allison Colorado, Broad Communications
Khalid Shakir is a principal software engineer in the McCarroll Lab.

Raised in a family of educators in Philadelphia, Khalid Shakir was exposed to both computational and biological sciences at a young age. His first scientific experiments involved tinkering with spare equipment from his parents’ high school classrooms including a Commodore 64 from his father’s computer lab and microscopes from his mother’s biology classroom. 

Now, Shakir has traded in his Commodore 64 for large-scale computational tools that he develops as a software engineer at the Broad Institute of MIT and Harvard. After earning a degree in Computer Science and working for multiple technology startups, Shakir first came to the Broad to work on a project studying human genetic variation called the 1000 Genomes Project, which launched in 2008. He was intrigued by the prospect of scaling computational tools to analyze ever-growing biological datasets. As part of the Data Sciences Platform, Shakir helped build Terra, an open-source, cloud-based biomedical data sharing platform.

Today, Khalid is a single-cell computational analysis specialist in the lab of Steve McCarroll within the Broad’s Stanley Center for Psychiatric Research. As part of the Broad's Center for Human Brain Variation, he builds computational tools to help scale up the BRAIN Initiative Cell Atlas Network (BICAN) project, which is studying 200 billion human brain cells to better understand cellular and molecular variation in healthy individuals.

Shakir is also a member of A4C, a Broad affinity group for people of African, African-American, and Afro-Caribbean descent. He hopes to use his connections within A4C to give back to future generations in the same way that his role models helped open doors to his dream career.

We spoke with Shakir about his interest in technology, tech trends he’s excited about, and his experience with A4C in this #WhyIScience Q&A.


Which sparked your interest first: technology and computer science, or biology?
I was really fortunate in that I was introduced to both from a young age. But I never thought about merging the two until just before I came to the Broad. I was talking to a Broadie working on the 1000 Genomes Project. They were telling me that the increased scale of sequencing required a lot of computing resources. I didn’t understand the biology at the level that they understood it, but I decided to join the team and combine my limited interest in biology with my extensive computer science skill set.

What are you especially proud of?
What I’m really proud of is that I work with so many smart people. The imposter syndrome is real, but because I’ve had a lot of experience with things like on-prem and the cloud [privately and publicly owned data centers], I’m able to be a tech translator for folks in the lab. I can show people how these tools work and what doesn’t work to help them save time. I’m helping computation move into the current decade where we’re using a variety of computing resources and making it more reusable.

We’re reusing open-source software that other people have built and adapting it to further bioinformatic science. And we keep on building new knowledge. It’s an exciting time. We have new tools, new amounts of hardware with the cloud, much bigger parallel computing capabilities. We are expanding knowledge at an unprecedented rate. I've really enjoyed working on that.

Are there any trends or emerging technologies that you’re particularly excited about?
I’ll say I’m excited about interactive visualizations, which are built on top of open source plotting packages such as R. They provide ways to not only display plots, but for people to click and interact with the plot and maybe discover new ways of interacting with the visualization. 

I’m also excited about AI. A year or two ago, everybody was talking about blockchain — that was a fad. But generative AI is here to stay. I think everyone has to learn how to use it, including understanding the privacy implications, how to prompt the algorithm, how to evaluate the outputs and know when it’s giving you “hallucinations” or made-up results. Software engineers, biologists, everyone will need to get comfortable with this new tool.

How has your involvement with A4C shaped your experience at the Broad?
In high school, I got a lot of help from teachers and local programs. There was a group called Concerned Black Men that gave me a scholarship to college, but there was another group that helped me practice with interviews. They had us dress up, show us how to tie a tie, and how to conduct ourselves in professional settings.

My interaction with A4C at Broad is sort of an echo of that. I have had so many more experienced people helping me out. Marianie Simeon [co-founder of A4C] is one of my role models and I appreciate what everyone on the A4C Steering Committee is doing. I hope that, as a part of A4C, I can give back in the same way that different organizations have helped me and be a familiar face for people inside the Broad. Because I’m not in the office and I spend so much time in front of the computer, I’m not bumping into people in the hallways. The A4C meetings create this additional community for people with common backgrounds and interests. I love the different affinity groups at the Broad for finding those bonds for people who may otherwise feel isolated or lonely within the wider organization.

What advice would you give students interested in careers in technology?
Look for the people who want to help. So many people want to help and give back, and they’re looking for you. There are so many people who can explain things better than a textbook. Even if you reach out to somebody and they can’t help you, they may put you in touch with someone who can.