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Apple Says New Power Mac G5 Quad Offers 39-Percent Speedup for Bioinformatics Apps

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Apple's recently launched Power Mac G5 Quad system offers a 39-percent speedup over Apple's previous Power Mac, the 2.7 GHz dual-processor Power Mac G5, when running bioinformatics applications, company officials said last week.

In a demonstration in Apple's New York briefing center, Todd Benjamin, product manager for the Power Mac G5, said that the system — which includes two 64-bit 2.5 GHz dual-core Power PC G5 processors — performed the Bioinformatics Benchmark System (BBSv3) from Scalable Informatics 39 percent faster than the previous Power Mac. BBSv3 runs version 2.2.11 of NCBI's Blast and version 2.3.2 of Hmmer.

The new system also offered a 22-percent speedup running Mathematica 5.2 and a 76-percent improvement on Apple's Xcode development software, Benjamin said.

The dual-core system doubles the processing power of its dual-processor predecessor, but that doesn't necessarily mean twice the performance, due to processing "overhead" for some applications, Benjamin said.

Elizabeth Kerr, director for the SciTech market at Apple, said that most multi-threaded applications for bioinformatics have been written for clusters — not dual-core processors — but noted that bench-top capability from systems like the G5 Quad should drive the development of more applications for the architecture. For example, she said, Wolfram Research has just released a multi-threaded version of Mathematica, which is expected to perform better on the dual-core system than version 5.2 did.

On the Linpack benchmark, the G5 Quad hit the 21-gigaflop mark, which is nearly twice as fast as the previous G5. In other benchmarking tests, the system demonstrated a performance of 76.6 gigaflops, compared to 41.1 gigaflops for the previous system.

The new system also supports Apple's first workstation graphics card — the Nvidia Quadro FX 4500, which enables stereo 3D visualization for applications in molecular modeling, crystallography, computational chemistry, and medical imaging.

Kerr said that a number of end-user scientists in the medical imaging community have developed their own visualization software for MRI data using the Xcode development environment. One such example, called OsiriX, compiles MRI scans into interactive 3D images, which users can share in real time with Apple's iChat AV, or store in iTunes to export to a video iPod.

Another program, the PyMol molecular graphics program from DeLano Scientific, has been upgraded to take advantage of the G5 Quad's stereo 3D visualization capabilities — a feature that enables users to better view the alignment of protein structures or the docking characteristics of small molecules within a 3D protein structure.

Pricing for the G5 Quad starts at $3,299.

— Bernadette Toner ([email protected])

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