Greg Caporaso launches bioinformatics courses

By Maria DiCosola
Journalism & Strategic Communications, 2014

Most university professors with a love for two different subjects develop those interests separately and then find a way to teach classes in two different colleges or departments. Northern Arizona University (NAU) Assistant Professor and Researcher Greg Caporaso, however, found a way to combine his two interests—biology and computer sciences—into one field: bioinformatics.  Soon, students with similar interests will be able to follow suit.

A new field for NAU

Greg Caporaso

Greg Caporaso: A champion of bioinformatics. Photo: IDEA Lab.

Bioinformatics, a field where researchers use computer-analyzed data to drive experiments and research within the biological and medical fields, is a new scientific direction for the university.

"The reason why this is emerging as an important field at this point in time is because biology is very rapidly becoming a data-intensive field," Caporaso said. "You learn pretty quickly that you can't open a 100-GB file in Excel."

Caporaso, who joined the computer sciences department in 2011, is the first NAU faculty member in this interdisciplinary field. He is developing a training program and course curriculum for both graduate and undergraduate students that will launch in 2013, although pilot courses are being offered.

Caporaso's plan is to first develop a minor in bioinformatics, which can be paired with either a biology or computer science major. In the meantime, Caporaso is introducing the idea of bioinformatics to biology and computer science students.

This fall, graduate students could take BIO599/CS499 Computational Biology: Addressing Biological Questions with Computing. "This is a projects-oriented course where students work in interdisciplinary teams to answer biological questions based on large genome, metagenome, or marker gene data sets," Caporaso explained. "Biology students are encouraged to bring their own questions and data (e.g., related to their dissertation project), in which case projects can be designed around those data sets. Alternatively, we work with existing biological data sets."

Other courses are being designed to get students comfortable with partnering the two sciences, such as developing practical computing skills for biologists, including how to do basic programing, how to run large programs on super computers, and how to use remote systems, such as the Amazon Compute Cloud, to analyze large amounts of data. More advanced courses focus on such topics as the design, implementation, and presentation of bioinformatics experiments.

Cross-disciplinary collaboration

Not surprisingly, Caporaso focuses on cross-disciplinary collaboration. He pairs biology students with computer science students to combine their skill sets. "My classes are usually split. I've got biology students and computer science students in the same class," Caporaso explained. "The biology students are definitely coming in more with research as a career goal, whereas my [computer science] students are generally interested in exploring [bioinformatics] as a career goal."

To succeed in the field of bioinformatics, a person needs to have skills in both disciplines, Caporaso said. "A lot of computer science students come at it thinking, ‘Okay. I just need to be able to write some Pearl Code or CC Code to be able to help people in this field.' The problem is that most of them have no idea of the complexity of biological systems. So, unless you can be thinking about how you might model something like that . . . unless you're thinking about the types of errors that might sneak in at the various steps, or understanding the steps, you can never actually build an accurate model of that system." Similarly, biology students need to have computer and programming knowledge to be able to manage the massive amounts of data they collect in the field.

"There are a lot of potential collaborations [at NAU], and there's a need for the types of students that I'm training here," Caporaso said. "So there's been a lot of enthusiasm [here at NAU] about this bioinformatics program that I'm developing."

Caporaso's research

Caporaso's interest in the subject of bioinformatics is not just theoretical: He is working on his own research project at NAU. Caporaso is analyzing data that shows a correlation between the bacteria in a person's stomach and the amount of calories that person extracts. "The ultimate goal with this type of work would be to figure out how you can alter the gut community to treat human disease, such as obesity," Caporaso explained. Computing helps to analyze the vast amounts of data generated to study the microbial communities.

Caporaso's work is one example of how being knowledgeable in both biology and computer science can be used to tackle complex problems with large sample sets that require in-depth analyses.  

Nanda Guddera, NAU Associate Vice President of Research, sees the need for data analysis in biology continuing to grow in all sectors of society, not just academia. "Bioinformaticians can find jobs in academia, they can find jobs in industry, in private start-up companies, in government . . . So, it's a global phenomenon. These days, informatics is used everywhere. It all comes down to data," he said.

Please Join the Conversation about Informatics

As data sets continue to increase exponentially in many different disciplines and areas of research, is informatics—big-data research—and the ability to use stored data to answer new research questions an important future direction for expanding the Northern Arizona University(NAU) research mission? Vice President for Research Bill Grabe would like to hear from NAU faculty about this issue. An informal meeting with interested faculty and staff is planned for early November. If you would like to join the conversation about informatics, please contact Grabe at William.Grabe@nau.edu

According to Grabe, some of the reasons why informatics could help NAU achieve important research growth include:

  1. Calls by NIH, NSF, and other federal agencies for these capabilities,
  2. Recognition by the Obama administration that this should be a research foundation for future science work,
  3. Major investments by many universities in this direction, and
  4. New research capabilities that will be viable and fundable at a university of NAU’s size and resources.

"A new strategic research direction does not mean that we would stop supporting our existing research strengths," Grabe explains, "but it does identify what may be the next core strength at NAU five to seven years from now."

 

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