Crunch time: The dual G5 tackles life sciences data

Computerworld - Apple Computer Inc. has been courting the life sciences market as a new business opportunity, given the Macintosh's operating system's Unix underpinnings and a wealth of open-source software. The combination of Apple's beautiful Aqua user interface with the FreeBSD base underpinning Mac OS X has made working with an Apple G4 a pleasure. And now comes the more powerful Power Mac G5.

As a life science researcher, I spend most of my time handling large amounts of data -- hundreds of thousands of database records in data sets that can reach 2GB in size and take two weeks to generate on a dual-processor Linux server. It's my job to design the experiments, use the right software to address questions, write scripts to control software tools, generate data, write more scripts to process that data, then load and present the results in a form that other researchers can understand.

Creating, parsing, compiling and sorting data takes time -- and processor power. The more power you have, the faster you can work. That's why Apple's G5 represents an important step forward for anyone with compute-intensive work. It's one intensely fast machine.

To do my work, I use a combination of Perl, the National Center for Biotechnology Information's (NCBI) BLAST program and FileMaker Pro. Perl 5.6, a popular and flexible programming language, is installed with Apple's Developer Tools, obtainable from the Apple Developer Connection. BLAST, which stands for Basic Local Alignment Search Tool, is a publicly available tool kit of applications for searching and comparing DNA and protein sequences. It's used extensively in the bio-IT field to match genes or DNA and protein sequences. The program is very processor-intensive (hence those two-week runs) and requires copious amounts of memory to handle those 2GB databases.

I also use BioPerl, a framework of modules that sits atop Perl and reduces the time needed to code various routines for handling life sciences data. Using Perl and BioPerl, I can write routines to control research programs like BLAST, and parse the information it generates.

Finally, FileMaker Pro is a great database tool for research groups. With personnel and time perennially short, simple solutions that require minimal effort are key. Less than an hour is needed to develop two elegant FileMaker Pro databases that can hold DNA sequence queries and their BLAST results. And it saves time when searching a database with almost 1 million records.

With that background, I put Apple's newest Power Mac G5, the dual 2-GHz model loaded with 2GB of SDRAM, to the test. I compared it with a late 2002 dual 1.25-GHz Power Mac G4 with 1GB of RAM. The model that has been discontinued has 2MB of Level 3 cache memory per processor and was the top-of-the-line model last fall.