Most biologists go to school to study biology. It is reasonable for them to assume when they got their degrees that a a functional familiarity with Microsoft Excel would be all the technological knowledge they would need to succeed in their career. But little did they know that supercomputing would, for some, become as ubiquitous to their toolset as a lab bench and a test tube. New areas of study, however, like bioinformatics often rely on massive, multi-gigabyte data sets. As a result, biologists increasingly find that access and ability to effectively use these new high-powered research computing tools have become an essential component of their work.
And this trend does not stop with biology. High performance computing is no stranger to those in research fields such as astrophysics and materials science. However, high performance computing is becoming a necessary research tool for researchers all across the university, including in fields such as marketing and economics where it was not historically used. As such, the specialized skills to work with giant data sets and supercomputers are becoming increasingly essential to conduct research.
Northwestern Information Technology’s Research Computing department enables researchers across the University to ask deeper questions and find answers they otherwise would not be able to by providing key resources for research – computing clusters, software, training, and perhaps most importantly, on-site consultants who provide face to face support. Led by Associate Director Joe Paris and Manager of Computing & Data Support Services Jackie Milhans, the Research Computing Services team facilitates research by regularly offering training workshops for the general Northwestern community as well as for specific programs or departments. The two main workshops series currently being offered are the Researcher's Toolkit workshop series, in partnership with the Northwestern University Libraries, and the Computational Skills for Informatics workshop series, in partnership with Galter Health Library.
The Researcher’s Toolkit workshop series offers a number of succinct, 1-2 hour interactive sessions on various topics that range from publishing skills to computer programming. Some topics include workshops on mobilizing research (how to use mobile devices for research purposes), creating academic social networks, and how to get resources for your research (i.e. funding). These short courses are an important first step for interested parties who don’t really know where to begin.
Beyond these, the series also runs workshops that focus on computing skills, such as introductions to Quest, the University’s supercomputing cluster, and to the R and Python languages. At Northwestern, some of the largest Quest communities of research are materials science, astrophysics, and genomics.
The Computational Skills for Informatics (CSI) series, offered in partnership with Pamela Shaw of the Galter Health Library, provides similar content intended for scholars in bioinformatics, a field that develops and uses computational methods and tools to interpret biological data.
Zexian Zeng, a Ph.D. candidate in Health and Biomedical Informatics at Feinberg, has been applying the skills he learned in the CSI Bioinformatics Workshop series to his research analyzing the impact of rare genetic variants on cardiomyopathy, a type of heart disease.
“Whole genome sequencing provides nearly complete coverage of the nearly three billion base pairs of the human genome with each base sequenced approximately 30 times. On average, around four million variants are detected per genome. With the massive amount of data, personal computational tools remain bottlenecks for population-based human genome study. The Bioinformatics Workshops provided me exposure to Quest, Northwestern’s high-performance computing cluster. Working within this cluster, I am able to investigate the role of human genetic variation, which is not possible with my personal computer alone," says Zexian.
Dr. Mark Mandel, Associate Professor at Feinberg in the Department of Microbiology-Immunology, has been working with the Research Computing department to offer specialized software classes for students, research staff, and faculty in a series called Programming for Biologists on the Chicago campus. These classes help build programming skills and the attendee’s ability to do research in a reproducible way. The focus is hands-on learning tailored to those individuals who have had no previous experience with programming languages.
“In addition to teaching the necessary programming skills, a major aim of these workshops is to provide a forum that the people around campus who are interested in and actively doing this type of work can connect with and learn from one another,” says Dr. Mandel.
Interested in research computing? Please contact Research Computing Services to ask a question or talk about your research challenges. See the schedule of trainings and events on the Research Computing Services website (http://www.it.northwestern.edu/research/). And don’t forget to join us at Computational Research Day in April 2017 to hear about research happening at Northwestern from faculty and students!