227-0085-36L Projects & Seminars: Genome Sequencing on Mobile Devices

Semester	Autumn Semester 2020
Lecturers	O. Mutlu
Periodicity	every semester recurring course
Language of instruction	English
Comment	Only for Electrical Engineering and Information Technology BSc. The course unit can only be taken once. Repeated enrollment in a later semester is not creditable.

Courses

Number	Title	Hours		Lecturers
227-0085-36 P	Projekte & Seminare: Genome Sequencing on Mobile Devices Groups are selected in myStudies. Für den Zugang zum Angebot und zur Einschreibung loggen Sie sich hier ein (mit Ihrem n.ETHZ account): https://psapp.ee.ethz.ch/ 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): https://psapp.ee.ethz.ch/ 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	3 hrs		O. Mutlu

Catalogue data

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.

Learning objective

Genome analysis is the foundation of many scientific and medical discoveries, and serves as a key enabler of personalized medicine. This analysis is currently limited by the inability of existing technologies to read an organism’s complete genome. Instead, a dedicated machine (called sequencer) extracts a large number of shorter random fragments of an organism’s DNA sequence, known as reads. Small, handheld sequencers such as ONT MinION and Flongle make it possible to sequence bacterial and viral genomes in the field, thus facilitating disease outbreak analyses such as COVID-19, Ebola, and Zika. However, large, capable computers are still needed to perform genome assembly, which tries to reassemble read fragments back into an entire genome sequence. This limits the benefits of mobile sequencing and may pose problems in rapid diagnosis of infectious diseases, tracking outbreaks, and near-patient testing. The problem is exacerbated in developing countries and during crises where access to the internet network, cloud services, or data centers is even more limited.

In this course, we will cover the basics of genome analysis to understand the speed-accuracy tradeoff in using computationally-lightweight heuristics versus accurate computationally-expensive algorithms. Such heuristic algorithms typically operate on a smaller dataset that can fit in the memory of today’s mobile device. Students will experimentally evaluate different heuristic algorithms and observe their effect on the end results. This evaluation will give the students the chance to carry out a hands-on project to implement one or more of these heuristic algorithms in their smartphones and help the society by enabling on-site analysis of genomic data.

Prerequisites of the course:
- No prior knowledge in bioinformatics or genome analysis is required.
- A good knowledge in C programming language and programming is required.
- Interest in making things efficient and solving problems

The course is conducted in English.

Course website: https://safari.ethz.ch/projects_and_seminars/doku.php?id=genome_seq_mobile

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

7. An example of a purely software method for fast genome sequence analysis: http://www.biomedcentral.com/content/pdf/1471-2164-14-S1-S13.pdf

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits	3 credits
Examiners	O. Mutlu
Type	ungraded semester performance
Language of examination	English
Repetition	Repetition only possible after re-enrolling for the course unit.

Learning materials

No public learning materials available.
Only public learning materials are listed.

Groups

	227-0085-36 P	Projekte & Seminare: Genome Sequencing on Mobile Devices
Group	G-01

Restrictions

General	: Special students and auditors need a special permission from the lecturers
Places	Limited number of places. Special selection procedure.
Beginning of registration period	Registration possible from 18.09.2020
Priority	Registration for the course unit is only possible for the primary target group
Primary target group	Electrical Engin. + Information Technology BSc (228000)
Waiting list	until 25.09.2020
End of registration period	Registration only possible until 25.09.2020

Offered in

Programme	Section	Type
Electrical Engineering and Information Technology Bachelor	Projects & Seminars Autum Semester 2020)	W