Apple Science and Technology News for 12-06-02

12-06-02 Bryan William Jones

O.K. folks, the latest update in the science and engineering markets begins with the announcement of new Powerbooks and iBooks. Briefly, the Powerbook has received faster G4 chips starting at 867 MHz and going to 1 GHz and we also have the ATI Mobility Radeon 9000 graphics chips resulting in impressive performance, but the biggest news with this update is the availability of built in Superdrives making these true mobile desktop replacements. With the iBook, we have faster G3 chips at 700 and 800 MHz, a larger available hard drive and the ATI Mobility Radeon 7500 graphics chip. All portables also have taken a price reduction of around $200 US bringing the iBook in under $1000 making it quite the bargain for portable users. In fact, I am typing this article on one of the new 800 MHz iBooks with the 12.1 inch screen and can attest that this is the best iBook yet with the graphics chip from the previous Powerbook now giving respectable graphics performance in a compact, inexpensive and portable package ideal for travel away from your desktop.

Important updates to note are the eagerly anticipated update for Endnote compatibility with Jaguar or 10.2. Another important update that brings Jaguar compatibility is the latest update to Matlab. Technical details may be found here. Finally we also have updates to a wonderful statistics program JMP and from OpenOSX, we have an update to GrassGIS bringing much needed stability, an all new Aqua interface and updates to the code making it at least 20% faster overall.

Going on to other announcements, we have from SoftIntegration the release of Ch SDK for Mac OS X. Ch is a superset of C/C++ interpreter. Ch SDK allows Ch scripts to interface C/C++ binary modules. The Ch Control System Toolkit is also now available.

For those molecular modeling aficionado’s out there, Wavefunction has just announced their flagship product, Spartan is now available on OS X. Wavefunction has been on the Mac platform for years now with a molecular modeling package called MacSpartan However, Spartan for OS X gives users access to features previously found only in higher end packages for SGI’s IRIX and such. Additionally, Mac users will appreciate the fully supported preemptive multitasking that Spartan for OS X provides. Before this, we could select the amount of processor time that Spartan could use manually, but anytime one ran a calculation, the computers performance in all other areas slowed to a crawl as Spartan gobbled up any available CPU cycles. By giving Spartan access to the maximum available CPU time, even checking email would prove to be impossible. With OS X and Spartan, the Macintosh really can replace two or three computers typically on the desk of folks that perform lots of molecular modeling. For instance, I have often seen an SGI for molecular modeling sitting next to a computer of another flavor intended for everyday use. Aside from the advantages of bringing Spartan to OS X, there are a number of other improvements such as new computational engines via collaborations with Q-Chem (LINK), and computational algorithms previously unavailable on the Macintosh such as the following from their press release: Density Functional methods [local, BP, BLYP, EDF1, and B3LYP]; Møller Plesset methods [MP2, MP3, MP4, and LMP2]; and Advanced Correlated methods [among others, CCSD, CCSD(T), G3, and G3(MP2)]. Additionally, a wide variety of Gaussian basis sets and pseudopotentials are available. In addition to the range of new methods, major improvements in the computational engines include analytical frequencies for Hartree-Fock and density functional models, resulting in speed increases of an order of magnitude for these calculations. Perhaps we can swing a review of this product in the coming weeks.

Moving on to molecular biology applications, we have the release of EnzymeX, a program designed to help molecular biologists determine which restriction enzymes they should use to cut the DNA region of interest by providing enzymatic properties from over 580 commercially available enzymes with buffer activity information, references of amino acid properties, codon tables and more.

Dauger Research has also updated cluster computation on the Mac with the latest release of Pooch giving us the opportunity to take advantage of multiprocessing and cluster computing in one API environment with the possibility of even multi-CPU machines appearing to be multiple nodes. Another innovation with the latest revision of Pooch is one of the first applications of Apple’s Rendezvous technology in science markets giving users the ability to use Rendezvous to enable discovery, resolution and registration of cluster nodes both locally and over the Internet. Rendezvous applications are just now being thought about and some are in the first steps of development at more than fifty companies, but science remains a huge untapped market for opportunities using Rendezvous. Particularly in vertical markets such as large biotech corporations and medicine for everything from cluster computing as Pooch has shown, to patient management and information retrieval as medical staff walk into a patients room creating opportunities for more precise pharmacological management and better outcomes with less morbidity.

In other exciting parallel computing news, Wolfram Research has just released a cluster computing option for licenses of Mathematica called gridMathematica allowing for users of Mathematica to get much faster answers to questions that can be attacked by parallel computation by employing a TCP/IP based networking solution for Mathematica that is platform independent with distributed memory as well.

With these announcements, it looks like cluster computing is finally coming of age on the Macintosh platform given the possibilities that OS X provides as the University of Colorado has recently installed a 30 node Xserve cluster and a colleague of mine formerly at the university here, Michael Giddings now at the University of North Carolina has also recently installed a 42 node cluster for bioinformatics/proteomics work. Hopefully, these clusters, along with those in the Appleseed cluster will be among the first of many Mac based clusters in science, industry and entertainment.

From the data presentation world, we also have good news of a classic data charting application, DeltaGraph 5.0 which will be coming to OS X in the first quarter of 2003 from SPSS and Redrock Software. Deltagraph has hundreds of chart types including 2-D and 3-D options and has been on the Macintosh platform before. As a past user of this application I can certainly say I am happy to have it back.

Finally, I would like to point out an article in Bio-IT world discussing the presence of Apple in the bioscience arena, applications for bioscience ported to OS X and some discussion of the Xserve.

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