Seq: a high-performance language for bioinformatics

Speaker: Ariya Shajii , MIT

Date: Monday, May 04, 2020

Time: 2:00 PM to 3:00 PM Note: all times are in the Eastern Time Zone

Public: Yes

Location: Zoom https://mit.zoom.us/j/536883569 Password 008943

Event Type: Seminar

Room Description: Zoom https://mit.zoom.us/j/536883569 Password 008943

Host: Julian Shun, MIT CSAIL

Contact: Julian Shun, jshun@mit.edu

Relevant URL: http://fast-code.csail.mit.edu/

Speaker URL: https://ars.me/

Speaker Photo:
None

Reminders to: fast-code-seminar@lists.csail.mit.edu, seminars@csail.mit.edu, pl@csail.mit.edu, commit@csail.mit.edu

Reminder Subject: TALK: Seq: a high-performance language for bioinformatics

Abstract: The scope and scale of biological data are increasing at an exponential rate, as technologies like next-generation sequencing are becoming radically cheaper and more prevalent. Over the last two decades, the cost of sequencing a genome has dropped from $100 million to nearly $100-a factor of over 10^6-and the amount of data to be analyzed has increased proportionally, necessitating high-performance tools and methods in order to keep pace. Here we introduce Seq, a high-performance, Pythonic language for bioinformatics and computational genomics, which bridges the gap between the performance of low-level languages like C and C++, and the ease-of-use of high-level languages like Python. The Seq compiler employs numerous domain-specific optimizations to often attain even better performance than hand-optimized implementations of many important algorithms, which we discuss and evaluate.

Bio: I'm a graduate student at MIT CSAIL focusing on computational genomics, working with Prof. Bonnie Berger and Prof. Saman Amarasinghe. More specifically, my graduate research involves developing fast, accurate and easy-to-use algorithms and software for processing the ever-increasing genomic data that is being produced. I focus mainly on third-generation sequencing data, and applications pertaining to it like sequence alignment, assembly, genotyping and phasing.

Research Areas:
Computational Biology, Programming Languages & Software

Impact Areas:
Big Data

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Created by Julian J. Shun at Wednesday, April 22, 2020 at 12:25 AM.