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227-0085-33L 3 Credits BSC D-ITET

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Projects & Seminars: Accelerating Genome Analysis with FPGAs, GPUs, and New Execution Paradigms

Projekte & Seminare: Accelerating Genome Analysis with FPGAs, GPUs, and New Execution Paradigms

Lecturers & Examiners: Dr. Mohammed H. K. Alser, Dr. Juan Gómez Luna

The course unit can only be taken once. Repeated enrollment in a later semester is not creditable.

VVZ CR n/a

Last Updated: 2026-02-05 16:21:48

Abstract

The category of "Laboratory Courses, Projects, Seminars" includes courses and laboratories in various formats designed to impart practical knowledge and skills. Moreover, these classes encourage independent experimentation and design, allow for explorative learning and teach the methodology of project work.

Objective

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. The course is conducted in English. Course website: https://safari.ethz.ch/projects_and_seminars/doku.php?id=bioinformatics

Resources

Lecture Notes

See:https://safari.ethz.ch/projects_and_seminars/doku.php?id=bioinformatics

Literature

Learning Materials =============== 1. A survey on accelerating genome analysis: https://arxiv.org/pdf/2008.00961 2. A detailed survey on the state-of-the-art algorithms for sequencing data: https://arxiv.org/pdf/2003.00110 3. 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 4. 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 5. An example of using a different computing paradigm for accelerating read mapping step and improving its energy consumption: https://arxiv.org/pdf/1708.04329 6. 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

General Information

Language: English
Levels: BSC
Frequency: Semesterly recurring

Examination

Type: ungraded semester performance

Registration & Places

Signup Start: 17.02.2023
Signup End: 03.03.2023

Course Components

Type	Title	Time & Place	Hours
practical/laboratory course	Projekte & Seminare: Accelerating Genome Analysis with FPGAs, GPUs, and New Execution Paradigms Für den Zugang zum Angebot und zur Einschreibung loggen Sie sich hier ein (mit Ihrem n.ETHZ account): Bitte beachten Sie, dass die Seite jeweils erst zwei Wochen vor Semesterbeginn zugänglich ist und im Verlauf des Semesters wieder abgeschaltet wird. Die Einschreibung ist nur von Freitag vor Semesterbeginn bis zum ersten Freitagmittag im Semester möglich. To access the offer and to enroll for courses log in (with your n.ethz account): Please note that the P&S-site is accessible no earlier than two weeks before the start of the semester until four weeks after the start of the semester. Enrollment is only possible from Friday before the start of the semester until noon of the first Friday in the semester. Time: to be arranged with each student Location: various	No time listed	3 h weekly

Offered In

Electrical Engineering and Information Technology Bachelor
- Laboratory Courses, Projects, Seminars (A minimum of 15 cp must be achieved in the category "Laboratory Courses, Projects, Seminars".)
  - Projects & Seminars (Enrolment is only possible for students in the BSc Electrical Engineering and Information Technology from Friday before the start of the semester. Places are allocated using the P&S application tool ( ). Please only enrol for P&S for which you apply via the tool.)