Bioinformatics institute sees advancement in research, evolution of center with help of TACC
Many of the Texas Advanced Computing Center's (TACC) feature stories highlight the impact of advanced computing for a specific research project. But for one of TACC's users, the introduction of advanced computing and computational expertise resulted in a fundamental shift in the direction of the institute.
"We're very excited about our experience working with TACC and have seen that the results make a huge difference in our research, our careers, and on shaping the development of our department, our center, and our institute," said Jing Su researcher in CBSB and assistant professor in the Department of Diagnostic Radiology.
Between 2014 and 2016, CBSB published nearly 10 research papers featuring research supported by Stampede—the 10th most powerful supercomputer in the nation. The most recent published in Scientific Reports, explores how the Center used mathematical models to explore the interactions between prostate cancer and immune microenvironment. The paper also details how they used these models to predict treatment outcomes for prostate cancer with androgen-deprivation therapy.
The Research
The CBSB creates a collaborative environment where researchers, including pathologists, mathematicians and clinical doctors, develop and apply novel systems bioinformatics methods and molecular diagnosis. Researchers also integrate these applications into clinics and disease monitoring.
The Center is divided into three areas: bioinformatics; systems medicine; and systems biology for regenerative medicine. Although this research is diverse, there are similarities in the way supercomputing contributes.
"TACC not only changed the way we work, but it also changed the way our institute works."For instance, the prostate cancer research, which falls under systems biology, uses agent based modeling to understand behaviors at the cellular level — pathways into the cell, and how cells interact with other cells at the cellular, tissue, and body level.
"We do a lot of agent based modeling which heavily relies on millions simulations. To get a reliable result, we have to repeat each computation at least 100 times. We want to explore the combinations and effects and different conditions and their results," Su said.
The same methods were used for the Center's research on cancer initiating cells in multiple myeloma, a type of cancer that occurs in the bone marrow. This research contributes to the development of precision medicine, which are individualized medical therapies based on specific patient features.
Su estimates that the CBSB has used millions of hours on Stampede over the years.
The History
The CBSB's partnership with TACC began five years ago in Houston. At the time, the center was operating out of the radiology department at Methodist Hospital. The researchers established a 48-core server for parallel computing, but they soon realized a need for more parallel power. After the director, Xiaobo Zhou visited TACC, he realized that computing resources could be beneficial to the Center.
"TACC not only changed the way we work, but it also changed the way our institute works. We moved from Houston to Wake Forest three years ago in 2013. And before we moved here, Wake Forest asked us what we needed. We told them that we need HPC— we use it everyday," Su said.
"Because we had the experience of working with TACC, we were able to work with Wake Forest colleagues and build the first in-house HPC cluster in the medical school," Su continued.
That cluster is called DEMON. The researchers at CBSB use the system for development purposes—to test code, find bugs, and modify it to prepare for using Stampede. While developing the system, Su consulted with TACC experts to help establish the system's infrastructure, hardware and software environment, and governance policy.
The NIH-funded LINCS, the Library of Integrated Network-based Cellular Signatures, is one of the major projects at CBSB, and is an international network to catalogue gene expression and cellular processes. CBSB provides a database to access data generated from TACC analyses, the data is used by researchers around the world.
Closer to home, however, Su says that the widespread use of supercomputers impacts both seasoned researchers in the field and even high school students who spend a summer at the Center.
"We are shaping the research paradigm in our institute and bringing many researchers to the advanced computing field," Su said. "We make advanced computing something that researchers can access and understand."
