Vertex Pharmaceuticals

Two Problems. One Solution.

A screenshot from Coot running on a Mac; the blue cage represents an electron density function; the yellow lines represent an atomic model. Coot is critical to the X-ray Crystallography Group’s workflow at Vertex, allowing scientists to interact with protein models visually.

Clarity in High-Resolution Visualization

Visualization is essential to both the iterative process and the dissemination of results. The high-end NVIDIA GeForce 6600 graphics cards included in Power Mac G5s are a necessity to running Coot and QUANTA properly. By combining Power Mac workstation systems with high-resolution Apple Cinema Displays, scientists can view up to 4-megapixels (2560x1600) of data at one time in stunning clarity across 30-inch of screen real estate. Vertix uses an open source molecular visualization system, PyMOL, to create 3D models to share results with other scientists. The discovery and decision process is dependant on carefully analyzing the visual representation of small molecule interactions — only the best displays are up to the task.

Cory Farinella led the effort to streamline the process of accessing the Structural Biology Group’s Linux cluster from Mac OS X by leveraging Open Directory and X Windows. “The applications that we migrated from SGI onto a high-performance Linux cluster run in Mac OS X from an X Windows session,” Farinella says. “Users can run applications off the cluster on their Macs, and it is seamless to the user. It works significantly better than the SGIs.”

Most applications, however, run natively in Mac OS X. Farinella continues, “It’s more on the Mac side; the important ones that run great on Apple are Coot — which is a big hit with our crystallography guys — and HKL and CCP4, which both run locally in X Windows on Mac.”

“I depend on Apple Remote Desktop — I wouldn’t be able to function without it. Version 3 is awesome.”

Farinella’s group is responsible for almost 500 Macs at Vertex, including a bevy of Power Macs and iMacs and about 100 PowerBooks. A few MacBook Pros have started to filter into the picture. They’re “smoking fast,” says Farinella.

Managing this number of computers requires a well-organized system with enterprise-class IT tools. “I depend on Apple Remote Desktop,” Farinella says. “I wouldn’t be able to function without it. Version 3 is awesome. One of the really key features I like about it is Curtain mode where you can block out the person’s screen and put up a little message telling them what you are doing. The package installer is a huge time-saver for us — I have packaged about fourteen of our applications — whereas we used to use installers on file shares which required users to run through the installers.”

Some day, Farinella hopes the company will move to 100-percent Mac, but in the meantime the cross-platform setup he has put in place works just fine. “I incorporated each user’s home directory — everything through Open Directory and Active Directory,” he explains. “Everything is now almost like one big super computer. When users save a file on their Mac Desktop, it is saved right on the cluster. Users can SSH in and execute what they want on the cluster or run most software directly on their system — it’s a large heterogeneous, integrated system now and they are all much happier users.”

More Time for Research

Vertex Pharmaceuticals focuses on society’s most critical health problems and Mac technology has been instrumental in improving productivity and allowing scientists to spend more time on this critical research.

“I think Mac OS X really surprises new users — even if you tell them about it for a while — you just can’t appreciate it until you sit down at a machine and use it yourself,” says Jacobs.

In an industry where it is common for IT administrators or users to have disagreements with management over computing platforms, everyone in Vertex’s management is agreement about Apple. “Our management is definitely partial to Macs — all our VPs have PowerBooks,” Farinella says. “I think there are a lot of people here excited about Apple.”

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