Gigabytes per second of DNA: using Rust for matching genomic motifs
by Martin Larralde
In a classic case of “Rewrite It In Rust”, implementing a novel algorithm for identifying binding sites in DNA led to a 100x improvement in speed. This talk emphasizes on what made it easier with Rust compared to C & C++, which are still in use predominantly in high-performance bioinformatics.
Speaker
Martin Larralde
Martin is a PhD student in Bioinformatics, originally from Paris. After starting his PhD at EMBL in Heidelberg in 2019, in co-supervision with ETH Zürich, he moved to the Leiden University Medical Center in 2024. Molecular Biologist and Computer Scientist by training, he used part of his PhD to write Python APIs for legacy C and C++ scientific code (PyHMMER, Pyrodigal), as well as new implementations for high-performance computing problems, where Rust is gaining traction. When he’s not writing code or research papers, he plays the bass and the guitar for a solo post-punk project.