Computational Biology
Empowering diverse young minds to apply computation to solve research-inspired questions in modern biology.
Program Overview
The Pre-College Program in Computational Biology offers comprehensive training in both state-of-the-art laboratory techniques for generating biological data and the computational methods necessary to analyze it.
Computer science has transformed biology and medicine. The next generation of life scientists must be well-versed not only in laboratory techniques for data generation but also in the computational skills needed to analyze and model this data. Pre-College Computational Biology provides high school students with an exceptional opportunity to explore this interdisciplinary relationship in a university setting.
Our program addresses key biological questions, including the study of microbes in Pittsburgh’s three rivers and the ongoing COVID-19 pandemic. After collecting water samples from one of these rivers, students will use modern laboratory techniques to isolate bacterial DNA, fragment it into millions of tiny strands, and sequence them. The challenge then becomes interpreting this vast amount of information - a task perfectly suited for computational biology.
The program is designed to highlight the synergy between experimentation and computational analysis in modern biology. Each day, students will spend half their time in a hackathon-style setting, working in small groups to develop code that solves computational problems, with guidance from instructors and teaching assistants. The other half of the day will be dedicated to laboratory work, where students will generate large datasets to be analyzed using their own code.
Carnegie Mellon University, a leader in automated science, offers students the unique opportunity to work with automation in an educational setting. Here, they will use robots (such as the Opentrons OT-2 liquid handling robot and custom hardware) to conduct experiments while learning how machine learning enhances experiment design and execution.
Curriculum
Programming Preparatory Materials
Preparatory materials will be provided from Professor Compeau’s Programming for Lovers open education project to admitted students in advance of the program to provide fundamental programming skills.
IMPORTANT: Admitted students will be required to complete some assignments taken from this project before starting the program.
Module 1: Metagenomics
- How do we design an experiment to learn about microbes in the environment?
- How do we collect samples from environmental water sources?
- How do we generate DNA sequence data from water samples?
- How can we extract DNA from samples with a variety of organic material with different structures (viruses, plants, bacteria, other microorganisms)?
- How can we use our knowledge of evolution and molecular biology to focus our experiments on studying bacteria?
- How can we use sequence data to determine the diversity of microbes in the rivers?
- How can we compare bacterial populations of two water samples?
- How can we determine what drives microbial diversity in river water?
Module 2: Sequence Alignment
- How can we isolate and identify individual bacteria in the laboratory?
- From bacteria, how do we isolate DNA?
- How can we match a DNA sequence to a database of known bacteria?
- How can we quantitatively determine the difference between two DNA strands containing only A’s, C’s, T’s, and G’s?
Module 3: Genome Assembly
- How can we break genomes into many small pieces for sequencing?
- How can we sequence very long strands of DNA?
- How do we assemble short strands of DNA to reconstruct genomes of organisms?
- With an assembled genome, how can identify genes and determine the function of those genes?
Module 4: Evolutionary Tree Construction
- What are the evolutionary relationships among bacteria in Pittsburgh’s rivers?
- Can we use evolutionary trees of viruses sampled from patients to determine the origin of SARS-CoV-2 in the U.S.?
- How can we visually compare multiple sequences to one another?
- How can we quickly determine where mutations in the coronavirus occurred and use this to identify variants?
Module 5: Automated Science
- How can we use liquid handling robots to improve the efficiency and precision of experimentation?
- How can we use robotics to help identify and isolate extremophile bacteria?
- How can we use machine learning to build a model to predict growth conditions for bacteria?
- How can we use artificial intelligence to direct experimentation to answer scientific questions?
Faculty Bio: Phillip Compeau
Phillip Compeau is Assistant Department Head and an Associate Teaching Professor in the Computational Biology Department. In addition to creating the PreCollege Program with Prof. Kangas, he is the founding director of the Undergraduate Program in Computational Biology. He is an award-winning teacher, and outside of the classroom, his educational materials have reached over a million learners and been adopted in 220 universities.
Faculty Bio: Joshua Kangas
Josh is an Associate Teaching Professor in the Computational Biology Department within the School of Computer Science. His teaching centers on equipping students with practical experience in experimental design and execution at the intersection of laboratory work (data generation) and computational analysis (data modeling and interpretation). In addition to co-founding the PreCollege Program in Computational Biology, he also serves as co-director of the M.S. Automated Science program, where he further trains students in the use of laboratory automation for generating biological data.
Application Details
Program Length |
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| Jun. 21 to Jul. 19, 2025 (4 weeks) |
Early Decision & International Applications Due |
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Scholarship¹ & Regular Decision Applications Due |
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Housing Options |
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Resident |
Eligibility and Application Requirements
Eligibility Requirements
To be eligible for Pre-College Computational Biology, students must:
- Be at least 16 years old by the program start date.
- Be a current sophomore or junior in high school at the time of application submission. Please note: Talented sophomores are encouraged to apply, however, most of our admitted students will be juniors.
- Have an academic average of B (3.0/4.0) or better.
Application Requirements
The complete application for Pre-College Computational Biology consists of the following:
- Completed online application
- Unofficial transcript
- Standardized test scores (optional)
- One letter of recommendation
- Responses to essay prompts
Application Essay Prompts
Essays are required for the following prompts (300-500 words each):
- What do you hope to gain from participating in Carnegie Mellon’s Pre-College Programs?
- Why are you interested in studying Computational Biology?
Frequently Asked Questions
What is computational biology?
Great question! The short answer is the application of high-powered computational approaches to analyze biological or medical datasets. For a lengthier explanation, check out the first 20 minutes of this video recorded by Professor Compeau.
Is this the right fit for me?
If you are good at math and love science, we think you’re in the right place.
Do I need to bring my own computer? What other supplies do I need?
Because our program is heavily dependent on coding, each student in our program will need to bring a laptop. We will provide all other resources needed.
Will I earn college credit from this program?
No, Pre-College Computational Biology students do not earn college credit.
Are international students allowed to participate?
Yes, our program is open to international students as long as they are able to enter the United States and come to Pittsburgh. They are not, however, eligible for scholarship consideration.