UT bioinformaticians bring life science researchers into age of big data

Sachit Saksena

Genomics. Transcriptomics. Proteomics. Researchers across campus need help with the advanced software necessary in a world of “-omics” technologies. 

The Center for Computational Biology and Bioinformatics (CCBB), under the leadership of Hans Hofmann, provides opportunities and support for investigators using computational approaches to research questions in the life sciences. Since 2012, the CCBB has offered a bioinformatics consulting group to meet the growing demands on campus, according to Dhivya Arasappan, one of the original members of the consulting group. Arasappan said they provide high-level analysis to deal with the data advanced hardware can now collect.

Another member of the consulting group, Dennis Wylie, started his career in industrial bioinformatics with biotechnology companies Seralogix and Asuragen, where he worked for seven years. He joined the CCBB in early 2015 to re-enter the academic world. 

Hofmann handpicked the members of the consulting group, such as Wylie and his colleague Benni Goetz, to provide the highest level of expertise. From walk-in consultations to long-term projects, the team offers varying levels of support for all inquiries. 

“For some groups, we do routine stuff that they don’t have the expertise for,” Wylie said. 

He said that in other situations, the team gets deeply involved and contributes ideas in a more meaningful way.

Wylie contributes most to a lab on campus that centers around protein degradation, where he looks at different characteristics of amino acid sequences. Otherwise, he specializes in statistics and machine learning. Goetz focuses on transcriptome assembly.

The group heavily facilitates the use of the Texas Advanced Computing Center (TACC), a group of supercomputers commissioned by UT-Austin. TACC provides the world’s eighth fastest supercomputing cluster. According to TACC’s website, one of the supercomputers can perform 10 quadrillion math operations a second.

“We have an incredible resource just available here with TACC,” Goetz said. “We are dealing with massive data sets … huge sequence files and big programs that would be impractical to run on a single computer.”  

The group would like to expand its reach. Many labs are heavily involved with the consulting group, but there are some labs on campus that could benefit from contacting the team, according to Wylie.

To take advantage of these services, researchers can contact consultants on the CCBB website. 

This year, the CCBB developed a new Freshman Research Initiative stream to introduce freshmen to computational biology and bioinformatics. In the stream, Big Data in Biology, Goetz, Wylie and the rest of their team teach undergraduates their specialized techniques. 

“We live in an era when it is possible to get much more deeply involved with this research much more easily than it ever has been,” Wylie said. “The FRI stream is a great way to get hands-on instruction in how to interact with this kind of data, because it can be very intimidating. This stream is a great way to stay current while you learn this type of analysis.” 

Because bioinformatics is at the cross section of computing, biology and statistics, this stream requires the freshmen to learn quickly. 

“We’re trying to provide basic introduction to these fields, but, more importantly, have them put it all together,” Goetz said. “The end goal is for the students to analyze real data and develop real research questions in the field.”

Goetz and Wylie, along with a large team at the CCBB, are working to bring life sciences research at UT up to speed in the growing world of computational biology and bioinformatics. 

“Pretty sure we’re going to make them all billionaires.” Goetz said.

Even if this doesn’t happen, Wylie said that the CCBB is still making a significant impact on the field.

“Understanding basic principles of computing and statistical analysis is valuable and is growing in importance in research,” Wylie said. “I think that medicine also stands to change a lot as a result of molecular research, and bioinformatics has a huge role to play.”