Part of the mission of the Library is connecting Health System affiliates with resources and expertise outside of the Library. On January 8th, Bart Ragon, Associate Director for Knowledge Integration, Research and Technology, and I sat down with three members of the University of Virginia Alliance for Computational Science & Engineering (UVACSE) team, Katherine Holcomb, Ed Hall, and Jackie Huband. We talked about their role at UVA and ways they can support the Health System.
How can someone from the Health System benefit from your services?
Katherine: We provide support for computational work. Each of us has a background in a discipline. For example, I have a background in Physics; Ed has a background in Signal and Image Processing; and Jackie’s background is Computational Mathematics. We can work with programmers in a large variety of fields because we focus on the programming aspect of projects. For Health Sciences, we could help someone write programs for data analysis or we can assist with projects such as getting a researcher set up to do large scale runs on clusters, either locally or at the national centers.
Jackie: We can help with data analysis or simply provide advice on statistical algorithms to use. Plus, we are looking into resources and tools for handling Big Data.
Ed: We can help with code development. Katherine and I serve as liaisons between the University and the national infrastructure XSEDE (Extreme Science and Engineering Discovery Environment) funded by the National Science Foundation (NSF). One of our main missions is to provide free consultations to University researchers. We can help to move their code from their desktops to our cluster and then, if necessary, scale up to the national level.
What disciplines do you work with the most and where is your potential growth?
Ed: We work with all science and engineering disciplines. Katherine and Jackie are beginning to work more with the social sciences and humanities, as those disciplines are becoming more quantitative. We have consulted with researchers in the Department of Biomedical Engineering, as well as reaching out to other Health Sciences departments.
Jackie: For example, we worked with a researcher in Neurosciences who wanted to create a 3D visualization of the inner-ear cells of a mouse, based on high-resolution microscopy images. Because the amount of data for the images was massive, the researcher was having trouble loading and viewing the images. We were able to install the recommended viewing tool on a more powerful computer and help the researcher (and his team) learn how to manipulate the images with the tool. We hope to increase visualization activities in the Health Sciences through our Visualization Lab, which is currently under construction and scheduled to open in the late spring.
Ed: Our educational mission addresses areas of potential growth. Every spring, the three of us co-teach a three-credit basic computational course for graduate students called Introduction to Computation as a Research Tool. It is designed to get students up to speed to do computational research. This course is an example of the educational activities designed to meet our mission of changing the culture of computation at UVA.
Are you changing that culture?
Katherine: Our biggest successes have been in training graduate students. In order for them to become comfortable with computation in their fields they must learn basic programming, as it is increasingly more difficult to rely solely on canned software packages. With our graduate course, and other educational activities such as our short courses and our High Performance Computing (HPC) Bootcamp, we have trained over 1,000 students.
Jackie: Our favorite example for changing the culture is a project that we worked on in the School of Medicine. The researchers were collecting and analyzing data by hand in Excel. We showed them how to write a program in R to process the data in a much more efficient way. What originally took her a few weeks to do by hand, she now does in less than six hours.
Did she write it in R?
Jackie: Yes. We started out by doing some of the coding for her, but along the way we provided training. She became excited about it and took the time to learn R on her own.
Katherine: People shouldn’t think of us as their programmers. Our goal is to jump-start a project. We often write a considerable amount of code in order to accomplish that; but once that is done, the researchers need to take responsibility for the project. Also, although we spend most of our time working with graduate students, we are happy to provide assistance at any professional level.
What contacts do you have at other UVA libraries?
Katherine: Ed and I used to be in the Brown Library’s Research Computing Lab, and we currently have contacts in the Scholars’ Lab and SciDaC. We’re hoping to collaborate with the two future hires for the library: a data mining specialist and a social sciences statistical consultant. We envision that they will use the higher performance resources and perhaps even participate as instructors for customized tracks in our graduate course.
Where do you see yourselves two years from now?
Katherine: We’ll be pushing into Big Data and visualization.
Jackie: We’re expecting the Visualization Lab to really catch on, leading to expansion in visualization resources.
Ed: And to have an academic culture that is much more aware of the value of more advanced computation.
Katherine: As a whole, the University of Virginia is lagging in this area. As the years go by we will help to build a computational culture that will better prepare our graduates for work within their fields and will help our researchers become more efficient and productive.