SAFARI Project & Seminars Courses (Spring 2023)

A genome encodes a set of instructions for performing some functions within our cells. Analyzing our genomes helps, for example, to determine differences in these instructions (known as genetic variations) from human to human that may cause diseases or different traits. One benefit of knowing the genetic variations is better understanding and diagnosis of diseases and the development of efficient drugs.

Computers are widely used to perform genome analysis using dedicated algorithms and data structures. However, timely analysis of genomic data remains a daunting challenge, due to the complex algorithms and large datasets used for the analysis. Increasing the number of processing cores used for genome analysis decreases the overall analysis time, but significantly escalates the cost of building, maintaining, and cooling such a computing cluster, as well as the power/energy consumed by the cluster. This is a critical shortcoming with respect to both energy production and environmental friendliness. Cloud computing platforms can be used as an alternative to distribute the workload, but transferring the data between the clinic and the cloud poses new privacy and legal concerns.

In this course, we will cover the basics of genome analysis to understand the computational steps of the entire pipeline and find the computational bottlenecks. Students will learn about the existing efforts for accelerating one or more of these steps and will have the chance to carry out a hands-on project to improve these efforts.

Prerequisites of the course:

• No prior knowledge in bioinformatics or genome analysis is required.
• Interest in making things efficient and solving problems.
• A basic knowledge in C or C++ programming language is required.
• Digital Design and Computer Architecture (or equivalent course) is preferred.
• Experience in at least one of the following is highly desirable: FPGA implementation and GPU programming.

The course is conducted in English.

Course description page
Moodle

Mentors

Lecture Playlist (Spring 2023):

Complete Lecture Playlist (Fall 2022):

• Introduction to Genome Sequence Analysis - Onur Mutlu:
  • Slides: PDF PPT
  • Video

• From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures:
  • Computational and Structural Biotechnology Journal , August 2022.
  • Paper PDFPreprint PDF
  • Talk Video (3 hours)
  • Slides: PDF PPTX

• Accelerating Genome Analysis: A Primer on an Ongoing Journey:
  • IEEE Micro (IEEE MICRO), Vol. 40, No. 5, pages 65-75, September/October 2020.
  • Slides: PDF PPTX
  • Talk Video (1 hour 2 minutes)

• GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis, Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
  • ARM Research Summit Talk Video (21 minutes)
  • MICRO'20 Full Talk Video (18 minutes)
  • MICRO'20 Lightning Talk Video (1.5 minutes)
  • ARM Research Summit Talk Slides PPTX PDF
  • MICRO'20 Full Talk Slides PPTX PDF
  • MICRO'20 Lightning Talk Slides PPTX PDF

• SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs, Bioinformatics, 2020.
  • Source Code
  • Online link at Bioinformatics Journal
  • Talk Video
  • Poster presentation at the Swiss Genomics Forum 2019, Geneva, 27 Sept 2019.
  • [Poster (pptx) (pdf)]
  • Poster presentation at ISMB/ECCB 2019, Basel, Switzerland July 21 - July 25.
  • [Poster (pptx) (pdf)]

• GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies, BMC Genomics, 2018.
  • [Proceedings of the 16th Asia Pacific Bioinformatics Conference (APBC), Yokohama, Japan, January 2018.
  • [Slides (pptx) (pdf)]
  • Source Code
  • arxiv.org Version (pdf)
  • Talk Video at AACBB 2019

• A survey on accelerating genome analysis: https://arxiv.org/pdf/2008.00961
• A detailed survey on the state-of-the-art algorithms for sequencing data: https://arxiv.org/pdf/2003.00110
• An example of how to accelerate genomic sequence matching by two orders of magnitude with the help of FPGAs or GPUs: https://arxiv.org/abs/1910.09020
• An example of how to accelerate read mapping step by an order of magnitude and without using hardware acceleration: https://arxiv.org/pdf/1912.08735
• An example of using a different computing paradigm for accelerating read mapping step and improving its energy consumption: https://arxiv.org/pdf/1708.04329
• Two examples on using software/hardware co-design to accelerate genomic sequence matching by two orders of magnitude: https://arxiv.org/abs/1604.01789 https://arxiv.org/abs/1809.07858