"We wanted to demonstrate that high-performance computing can be integrated into an iterative workflow because this is the way biologists really work," Oehmen said. "It was the MeDICi middleware that really helped us pull the various data, analysis, and visualization together."
In genomic studies, computer programs compare DNA sequences of different living things to find shared proteins or uncover the function of a mystery protein, generating ideas that can then be tested in laboratory experiments. This interactive program gives laboratory researchers a place to start in looking for proteins and genes with interesting functions.
Oehmen demonstrated that their interactive program and high computing power could explore the complement of proteins found in an organism, allow them to focus on a protein that intrigued them, and investigate its possibilities.
Browsing through all the proteins in various Shewanella bacterial species, the team noticed more proteins than expected with tell-tale iron-detecting components.
"We thought, there are a lot of iron-sensing proteins here. What are they doing?" said Oehmen.
As it happens, many species of Shewanella have the ability to transfer electrons to an electrode, thus forming a simple biological fuel cell, an alternate means of generating energy. Iron is involved in this activity, so the team decided to identify proteins that may help the bacteria sense the iron and form a biofilm on an electrode.
Starting with a known, non-Shewanella protein that senses iron, the program allowed researchers to guide the search for similar proteins out of 42,000 proteins from 10 Shewanella species. After rounding up about 550 possible iron-sensing proteins, the researchers switched gears and determined which of these might also be invo
|Contact: Mary Beckman|
DOE/Pacific Northwest National Laboratory