Harvard Medical School – Algorithmic Optimization

Optimizing DNA Sequencing with the power of the crowd. See how a 2-week long algorithmic challenge delivered an extreme value outcome powered by data science.

Project Details

Studying the human genome is the world’s largest project. The genome (DNA code) of every individual is unique. The sequencing of the human genome holds benefits for many fields, from molecular medicine to the study of human evolution. The process of identifying the boundaries between genes and other features in a raw DNA sequence is slow work, even when computer programs are used to meet high throughput demands.

PROBLEM

The process of identifying the boundaries between genes and other features in a raw DNA sequence is slow work, even when computer programs are used to meet high throughput demands. The goal of the DNA Edit Distance Challenge was to speed up the process of standard DNA sequencing — the distance between strings — which is critical for making high-precision, high throughput readouts of the immune system.

THE SOLUTION

The Topcoder result was extraordinary — it reduced the speed from 260.4 minutes to 16 seconds — 976 times faster than a government sponsored algorithm and even a paradigm shift from Harvard’s attempt to quicken its pace using a full-time employee. This extreme value outcome represents a shift in how Harvard will approach the present and future of its genetics research.

CLIENT

Harvard Medical School is renowned for its innovation in medical research, including genomics. It approaches the study of genetics as a unified way to extract organizing principles for understanding biology and other fields.

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Faster than original algorithmic solution

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WINNING COUNTRIES
“Topcoder (Appirio’s community) surpassed expectations: a two-week competition led to code that was just as good but almost three orders of magnitude faster for a few thousand dollars. Hard to imagine beating that.”

Ramy Arnaout MD, DPhil, Associate Director

Clinical Microbiology, Department of Pathology, BIDMC