Crunch time: The dual G5 tackles life sciences data

Bob Freeman   Today’s Top Stories   or  Other Macintosh OS Stories  

Advances in SSL and Certificate Management Virtualization: Simplify. Automate. Lower Costs. Mobile Device Management: Wresting Order from Chaos 7 Requirements of Data Loss Prevention Ponemon Study: How much does a data breach "cost"? E-LOAN maintains reputation as a privacy leader with Symantec Data Loss Prevention solutions Virtual Reality SaaS Solutions for Remote Systems Management Mobility @ the Speed of Business Sign up to receive Macintosh OS Resource Alerts

October 9, 2003 (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

Continued...
1 | 2 | 3 | 4 | NEXT  

Print this Story

Send Us Feedback

E-mail this Story

Digg this Story

Slashdot this Story

Review: Hands on with the 12-inch PowerBook Hands-on: Airport Extreme a bit too far ahead of curve? Crunch time: The dual G5 tackles life sciences data

Second look: Apple's dual 2-GHz G5 by the numbers Update: Apple's PowerBook 17 stretches 'laptop' moniker First take: Our look at Apple's Dual 2-GHz G5

"The new MacBook Pro spy shot looks very real. Let's take a look at what we can ascertain from it......" Read more... Read more Macintosh & Apple posts or See all Blogs

Feds considering changes to H-1B application process in wake of report Exploit code loose for six-month-old Windows bug With market meltdown, which tech firms become predator or prey? More top stories...

The Grill: Privacy is a thing of the past, says private investigator Report: World Bank servers breached repeatedly Apple asks judge to make iPhone lawsuit moot

Health hazards for IT workers -- how that desk job wears your body down Too much junk food, too little exercise and a 24/7 tether to technology? Your body ain't happy, friend. Let us count the pains. NASA robot sends back evidence it's snowing on Mars Instruments on the surface of Mars have detected falling snow that is likely evaporating before it reaches the planet. Wall Street's collapse may be computer science's gain One positive development stemming from the collapse of Wall Street may be a boost in interest in computer science and IT careers among students who were previously interested in financial services jobs. Installing Linux apps: A few good tips Getting new software installed on Linux doesn't have to be hard, but it can differ depending on what you're installing. Windows Vista A to Z Reviews, analyses, how-tos, visual tours, hot issues and predictions about Microsoft's new OS. More Continuing Coverage After 9/11: Homeland Security Apple's iPhone Ask a Premier 100 IT Leader Bill Gates steps down BlackBerry Legal Battle Data Security Breaches Electronic Voting Firefox H-1B Visas HP's Boardroom Scandal Handheld Devices Hurricane Katrina Aftermath Microsoft Legal Issues Microsoft's Vista Open Source RFID Technology SCO's Linux Fight Sarbanes-Oxley Act Spam Voice Over IP Wi-Fi Windows Meta File Vulnerability Windows XP Service Pack 3 IT Careers 2010 Four years from now, the IT field will be a vastly different place. Will you be ready? More Special Reports Premier 100 IT Leaders 2007 Best in Class 2006 Computerworld Horizon Awards 2006 Premier 100 IT Leaders 2006 Salary Survey 2007 Best Places to Work in IT 2007 IT Forecast 2007 Premier 100 IT Leaders 40 Years of Computerworld ASPs, Take Two Best Places to Work in IT 2003 Best Places to Work in IT 2004 Best Places to Work in IT 2005 Best Places to Work in IT 2006 Business Intelligence Home Runs Business Intelligence: Smarter BI Business Intelligence: The Future of BI CRM Goes Vertical CRM: Sober CRM Career Planning Guide 2005 Careers: IT Profession 2010 Computerworld Horizon Awards 2005 Data Management: Mining for Gems Data Management: Taming Data Chaos Development: Hard-Workin' Web Sites Development: New Tools New Choices Development: The New World of Application Development Development: The Web Services Tsunami Development: Web Services Hurdles Disaster Recovery: Preparing for the Worst E-commerce Grows Up E-mail/Groupware: Big Decisions Faces of Mobile IT Forecast 2006 Global Mobile Hardware: Multiple Cores, Multiple Challenges Hardware: On-Demand Un-Hyped Hardware: The Shape of Things to Come Horizon Awards: 10 Cool Cutting Edge Technologies IT Management: Guide to Managing Vendors IT Management: Navigating Global IT IT Management: Recovery Ahead IT Management: The Future of IT IT Management: The Resourceful Project Manager Innovative Technology Awards 2004 Management: Reinventing IT Microsoft in Transition Mobile/Wireless Leaders and Laggards Mobile/Wireless: The Untethered Worker Mobile/Wireless: Tiny Gadgets, Huge Costs Network Management: Taking Control Networking: Turbulence Ahead! Networking: VoIP Goes Mainstream Operating Systems: In the Slow Lane Operating Systems: Linux Goes Global Operating Systems: Should You Nix Unix? Outsourcing: Offshore Buyer's Guide Outsourcing: Outsourcing Dangers Premier 100 IT Leaders 2004 Best in Class Premier 100 IT Leaders 2005 Best in Class ROI: Do the Math! Salary Survey 2003 Salary Survey 2004 Salary Survey 2005 Security Action Plan Security: Compliance Headaches Security: Proactive Security Security: Risk and Reward Security: Tips From Security Pros Souped-up Security Storage: Battling Complexity Storage: Cheap & Secure Data Stores Storage: Stretching Your Storage Dollars Storage: The Lean Storage Machine Storage: The New Rules of Storage Storage: The Ultimate Backup Guide Supply Chain: Missing Links Supply Chain: RFID Reality Check The Business of Security Web 2.0 Security Wireless: Wireless At Work All Zones Application Performance Zone Business Continuity Zone The File Data Management Zone Security Management Zone The SAS Zone Business Intelligence and Analytics Zone Windows Protection Zone The Enterprise Search Zone Software as a Service Zone The Security Zone See your link here

Long Tail Supplier Collaboration - What's In It For You? Long Tail Supplier Collaboration - What's In It For You? Download this webcast, free, compliments of Sterling Commerce Go to the webcast  White Papers Read up on the latest ideas and technologies from companies that sell hardware, software and services. Business Transaction Management: Facilitating the Management of Virtual Environments Quick Sizing Guide for SAS Grid Running on HP BladeSystems and EVA Storage Prudential Financial protects its brand with Symantec Data Loss Prevention solutions View more whitepapers  Linux Rising Get this Computerworld report free (a $195 value) for a limited time, compliments of Novell. Linux is now firmly entrenched in the enterprise. Computerworld's new Executive Bulletin on the open-source operating system will get IT managers up to speed on the latest Linux developments, ranging from its impact on database sales to competition with other operating systems. Download this executive briefing  Virtualization Everywhere Download this white paper, free, compliments of Citrix. (Source: Citrix) Adoption of virtualization is concentrated among large enterprises, while adoption by mid-sized companies has been much slower. For these companies, the cost and complexity of server virtualization solutions has been a barrier. In this paper, we'll discuss how Citrix XenServer" provides simple, economical server virtualization for any size company. Download now! Download this white paper

• Review: Hands on with the 12-inch PowerBook
• Second look: Apple's dual 2-GHz G5 by the numbers
• Hands-on: Airport Extreme a bit too far ahead of curve?
• Update: Apple's PowerBook 17 stretches 'laptop' moniker
• Crunch time: The dual G5 tackles life sciences data
• First take: Our look at Apple's Dual 2-GHz G5

• Feds considering changes to H-1B application process in wake of report
• The Grill: Privacy is a thing of the past, says private investigator
• Exploit code loose for six-month-old Windows bug
• More top stories 

Best Places to Work in IT Where can you earn top dollar, get the best benefits, the latest IT and more? Find out in our 14th annual survey.

Preston Gralla: Apple plays the bully again Apple is once again unleashing its attack dog lawyers. This time against a college for using an apple in its logo. ... [more]