Columbia CS class among first students to experiment with mobile DNA sequencing device
Real-time mobile DNA sequencing is right around the corner, made possible by new hand-held, low-cost sequencing devices that can be carried or installed almost anywhere. These devices, still under development, will have a major impact on health, biology, forensics, and security. Seven of these devices are being made available to Columbia students in Ubiquitous Genomics, a computer science class offered this fall by Dr. Yaniv Erlich, who is structuring the class around the device to challenge students to imagine new applications and new methods to analyze DNA data.
DNA sequencing technologies are advancing at a breathtaking pace, faster even than Moore’s law, revolutionizing multiple domains from personalized medicine to forensics. Columbia computer science students are being given a unique opportunity to participate in a direct, hands-on way at an early stage of this new technology.
Ubiquitous Genomics, a class offered this fall by Dr. Yaniv Erlich, will focus on the newest phase of the DNA sequencing revolution: the advent of mobile DNA sequencing that makes rapid genomic testing possible from almost any location.
The technology is still too new to fully predict all its possible applications, but it’s easy to imagine police being able to analyze DNA evidence at a crime scene and doing it in real time to identify suspects before they can flee, destroy evidence, or mount another attack. Forensics is just the start. Health-related fields will also benefit when it becomes possible to quickly—without waiting for lab results—determine whether water towers harbor legionella, detect the accumulation of pathogenic microbes in meat, and perform diagnoses in the field during humanitarian crises. Mobile DNA sequencing will have applications in the home also. Erlich in his paper A Vision for Ubiquitous Sequencing (to be published in Genome Research this fall) even anticipates toilet systems equipped with DNA sequencing technology to trace the gut microbiome.
Mobile DNA sequencing is being made possible through a new generation of small, hand-held, and low-cost devices that plug into the USB drive of a PC and read DNA information in real time from samples taken on the spot. The devices are still under development and are being selectively distributed to researchers for testing and evaluation.
Columbia students are among the first students to have access to these devices as part of their training. Seven MinIONTM devices are being provided for use in Ubiquitous Genomics at no cost by the British-based manufacturer Oxford Nanopore after a request from Erlich.
The idea is to get the devices into the hands of the students to see what they can do with it, both to imagine new applications and come up with new methods or algorithms to analyze the data. (Any new software developed will be open source, licensed under GNU General Public License v2. Anyone wanting to use or modify the code must post it under the same license.)
“What happens when you give young, smart students a new device with tremendous potential? What are the new applications they can came up with?” wonders Erlich, who knows of no other class where students are getting this device as an integrated part of the curriculum. The students themselves did not know about the devices when signing up for the class.
Ubiquitous Genomics itself combines several aspects of computer science, including biology, electrical engineering, data science, and algorithms and software. While the first few weeks will cover the basics of traditional DNA sequencing and the special challenges of acquiring, storing, and analyzing huge amounts of genomic data (which can exceed the size of data sets in astronomy), the class will quickly shift to nanopore sequencing, the technology employed by the mobile sequencing devices. (Nanopore sequencing works by measuring electrical resistance as a DNA fragment passes through biological pore.) The class of 26, which includes both graduate and undergraduate students, will share seven devices and work together in groups of three and four to sequence and analyze DNA and do experiments that involve both the application side and the data side. Two hackathons count for half of the grade.
In structuring Ubiquitous Genomics around the device and assigning experiments and homework assignments based on these devices, Erlich is on the leading strand of educational methods. “I am very excited that we can bring this technology to the class. The aim is to build upon the creativity of our students and let them explore this revolutionary technology.”
A future article will report back on the student projects.
Dean Boyce's statement on amicus brief filed by President Bollinger
President Bollinger announced that Columbia University along with many other academic institutions (sixteen, including all Ivy League universities) filed an amicus brief in the U.S. District Court for the Eastern District of New York challenging the Executive Order regarding immigrants from seven designated countries and refugees. Among other things, the brief asserts that “safety and security concerns can be addressed in a manner that is consistent with the values America has always stood for, including the free flow of ideas and people across borders and the welcoming of immigrants to our universities.”
This recent action provides a moment for us to collectively reflect on our community within Columbia Engineering and the importance of our commitment to maintaining an open and welcoming community for all students, faculty, researchers and administrative staff. As a School of Engineering and Applied Science, we are fortunate to attract students and faculty from diverse backgrounds, from across the country, and from around the world. It is a great benefit to be able to gather engineers and scientists of so many different perspectives and talents – all with a commitment to learning, a focus on pushing the frontiers of knowledge and discovery, and with a passion for translating our work to impact humanity.
I am proud of our community, and wish to take this opportunity to reinforce our collective commitment to maintaining an open and collegial environment. We are fortunate to have the privilege to learn from one another, and to study, work, and live together in such a dynamic and vibrant place as Columbia.
Mary C. Boyce
Dean of Engineering
Morris A. and Alma Schapiro Professor