BioIT World Gene Browser with a Google Feel
*By Laurie Wiegler* *March 1, 2008* | Following the launch last year of ECell 3D, Kazaharu Arakawa of Keio University in Japan has launched another colorful and intuitive bioinformatics tool. Drawing inspiration from iTunes and Google Maps, the database browser, called Genome Projector (www.g-language.org/GenomeProjector/ <http://www.g-language.org/GenomeProjector/>), was developed at Keio’s Institute for Advanced Biosciences over the past year. As a highly visual and searchable genome browser with zoomable user interface, Genome Projector contains four “maps:” Genome Map, Plasmid Map, DNA Walk, and Pathway Map. Each map indicates genes in various colors, such as rRNA in red stripes and tRNA in green stripes in the Genome Map. Genome Projector currently lists some 320 circular bacterial genomes, reflecting Arakawa’s research interests, but may be expanded to include eukaryotes. Design was important to Arakawa. He’s a fan of Apple software because it traditionally sports an intuitive user interface. “This is often not the case for bioinformatics software and databases,” he says. “[I] borrowed color schemes and layout [from iTunes],” Arakawa says, adding that he was also inspired by Google Maps, from which he plucked its free API for the project design. His inspiration, however, was a Roche biochemical pathways chart. As an undergraduate, he was fascinated by the metabolism wallchart. It seemed to him “the grand sum of the history of biochemistry,” he recalls. He “almost trembled with excitement to start afresh in systems biology, to build dynamic cellular simulations on top of this knowledge.” The result of that fervor is Genome Projector. The G-language-powered database browser uses a Restauro-G back end to annotate the genome by similarity searches using the BLAST-Like Alignment Tool, connecting with protein databases such as UniProt Knowledgebase and NCBI nr. The front end boasts Web 2.0 technologies such as AJAX and EXT 2.0 framework. *Distinguishing Itself *Genome Projector resembles Cold Spring Harbor researcher Lincoln Stein’s GBrowse, although the two browsers do differ. For example, Arakawa says browsers such as GBrowse are designed to be scalable interfaces but require several user interactions, and are not genuinely zoomable user interface (ZUI) applications.
Arakawa debuted ECell 3D at a packed house at an Intelligent Systems in Molecular Biology conference workshop last July in Vienna. Like Genome Projector, ECell 3D is a bioinformatics tool with a focus on ease of use. “In my experience, [the] modeling process is mostly heuristic, with numerous trials and errors to get the model to work right, to sufficiently capture the cellular behavior that a scientist wants to test and learn,” says Arakawa. Therefore, good user interface and design that supports this process, such as ECell 3D for simulation results, and Genome Projector for data mining and searching, are essential.” ECell 3D boasts an interface that enables researchers to model cellular systems in 3-D graphics. The resulting platform, controlled by Bluetooth, is strikingly visual, looking much like a flight pattern or constellation map. Arakawa hopes to start integrating the software tools he’s developed so far to create a prototype modeling environment around ECell and hopes to achieve a “sophisticated environment” for modeling in systems biology. “There are a number of cell simulators already available,” says Arakawa, but he believes “Automation through knowledge integration for modeling is a key step for the success of systems biology.” -- L.W.
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