Four Ohio Supercomputer Center (OSC) employees, as well as two Ohio State University (OSU) plant biology researchers, had a manuscript published in the online journal, Plant Physiology. The manuscript was entitled, “Genome-wide Identification of Arabidopsis Coiled-coil Proteins and Establishment of the ARABI-COIL Database.”
OSC’s Bioinformatics Group, comprised of Dr. Eric Stahlberg, Senior Systems Manager, Shannon Schraegle, Webmaster and Bioinformatics Research Specialist, Shankar Manikantan, OSU Graduate Research Associate, and Mike Maloy, Student Programmer, worked on the database, which helps identify and browse Arabidopsis long coiled-coil proteins offering more narrow searches of coiled-coil features. Long coiled-coil proteins are important for the spatial organization of cellular processes.
“This database allows us to quickly gain and compare prediction data without submitting the sequence to a number of individual prediction servers,” said Dr. Annkatrin Rose, ARABI-COIL Postdoctoral Researcher and OSU Plant Biology Researcher.
By hosting the ARABI-COIL database, OSC will become more visible in the research community, encouraging other researchers to coordinate projects with OSC’s Bioinformatics Group, Rose said.
In 2001, Stahlberg was approached by Dr. Iris Meier, ARABI-COIL Principal Investigator and OSU Plant Biology Researcher, to identify Arabidopsis proteins predicted to form coiled-coil structures. The large number of sequences to be processed prevented Meier from performing the analysis on her lab computers.
“Meier was interested in the results of running the Multicoil program on 25,000 sequences,” Stahlberg said, “but was limited to web-only single sequences with her computers.”
Stahlberg explored resources for the project and found that OSC’s 32-processor SGI Origin 2000 system could easily process the amount of data within a few hours.
“I investigated whether we could download the program and run it at OSC,” said Stalhberg, “and we could.”
Stahlberg developed a Java program suite to analyze the computed output and convert important features to XML representation. His primary function was to guide the combined project’s IT development.
After demonstrating some initial runs at OSC, Stahlberg publicized the project, asking fellow employees to participate.
“Eric talked to me about the project. I had some Java background and it was very interesting, so I got involved,” said Manikantan.
Manikantan set up and maintained a MySQL database that was established on an OSC server and made available to the public through the ARABI-COIL website.
Maloy wrote software that migrated the Arabidopsis data into the MySQL database. He became interested because “it was an opportunity to work with a database system and experiment with some of my ideas,” Maloy said.
Schraegle became involved because of her strong science background. “I downloaded the GenBank protein sequences for the database and designed the website,” Schraegle said.
“The online database will bring additional recognition to OSC and show what the Center has to offer the research community,” Stahlberg added.
References:
Ethan Wolf, Peter S. Kim, and Bonnie Berger, "MultiCoil: A Program for Predicting Two- and Three-Stranded Coiled Coils", Protein Science 6:1179-1189. June 1997.
