Cornell University MacCHESS Facility
Researcher Brings Open-Source Software to the Mac
Bringing Standard UNIX Tools to Mac OS X
Through the GNU-Darwin project, Dr. Love aims to help Apple users by building on the unique capabilities of the Mac platform and providing free software to researchers who prefer the Mac. At the GNU-Darwin website, Mac-based researchers can download free scientific software packages such as PyMOL, a popular molecular modeling graphics package. “We help Apple users who, like many scientists, are already UNIX savvy. Using software from GNU-Darwin, they are able to work quickly and efficiently on the Mac with familiar tools,” explains Dr. Love.
“PyMOL on a Power Mac should run as fast or faster than on anything else — even high-end workstations.”
— Dr. Warren DeLano, Informatics Scientist, Sunesis Pharmaceuticals, Inc.
Dr. Love has also ported the FreeBSD Ports and Packages Collection over to Mac OS X. Typically, installing new UNIX software requires a number of time-consuming steps including downloading and unpacking the software, locating the documentation, compiling and testing the software. Using the Ports and Packages Collection, installing a new application can be carried out with a single command, further spurring the growth of the standard UNIX infrastructure on Mac OS X.
Dr. Love’s software development efforts have even attracted the attention of freeware publishers. PrimeTime Freeware published the FreeBSD Ports and Packages Collection as TDC, a set of Mac OS X compatible packages and source code. TDC brings thousands of standard UNIX tools to the Darwin-based operating systems including GNU-Darwin and Mac OS X. The entire TDC source code tree is also available from the GNU-Darwin website through SourceForge.
A Fast Platform for Molecular Graphics
According to Dr. Love, porting the FreeBSD ports system to Mac OS X was relatively fast and easy. Within a few months, Dr. Love had ported the FreeBSD packaging applications, and other components of the Ports and Packages Collection complete with an array of free custom software enhancements.
Other scientists are working to bring important research packages over to Mac OS X as well. Dr. Warren DeLano, an informatics scientist for Sunesis Pharmaceuticals, Inc. is using the standard development tools that come with Mac OS X to port PyMOL to Mac OS X. He wants to take full advantage of the hardware acceleration and OpenGL drivers available on the Mac. He prefers developing on Mac OS X because it is a stable, robust platform with a more elegant interface than standard UNIX. When the port is complete, researchers will have access to a Mac OS X native version of this popular molecular modeling tool, used in many areas of structural genomics such as protein crystallography, protein folding studies, and drug discovery. “PyMOL on Mac OS X will take full advantage of the accelerated graphics chip of the Power Mac, resulting in an incredibly fast platform for molecular graphics,” says DeLano. “PyMOL on a Power Mac should run as fast or faster than on anything else — even high-end workstations.”
As more researchers port popular open-source tools to Mac OS X, the Mac is becoming an increasingly attractive platform for scientists. It offers the flexibility and power of a standard UNIX OS, with its capabilities for clustering and compute farms, combined with a great array of development tools and advanced hardware capabilities such as graphics acceleration. For structural genomics researchers like Dr. Love and Dr. DeLano, the Macintosh is quickly becoming the only computer they need.
