Drug Scientists Slow to Adopt Open Source

A surge in open-source technology offers many businesses a potent combination of power and low cost, but the pharmaceutical industry remains well behind the curve.

That was the message at a session on data visualization and integration at a semiannual meeting of the nation’s chemists in Washington last week.

No one thinks open source can fill everyone’s software needs, but a “forceful” open-source community could create modules that bridge gaps in existing software designed for the pharmaceutical industry and help it become more efficient, said presenters. Yet so far, few are stepping up to the plate.

Interest in visualization software has surged in the pharmaceutical industry in the past couple years, but interest in open source has not, said Carol Rozwell, vice president of life sciences at consultancy Gartner Inc., who did not attend the session. However, she said, interest might pick up as the pharmaceutical industry sees IT more firmly integrated into drug discovery and development.

In a recent survey, Rozwell’s group looked at all sorts of software used by biopharmaceutical companies to find out if it was developed in-house or purchased from a software vendor.

Overall, there was an increasing tendency to use off-the-shelf products. “The one holdout area,” she said, “was discovery. Many clients express concern that the commercial products don’t quite fit the bill, hence the tendency to believe that the only option is to develop their own software.”

Software can come from pharmaceutical companies’ internal efforts, commercial software vendors, academics and open-source communities.

Each has its place, and its pitfalls, said Warren Delano, head of Delano Scientific, who presented his open-source product PyMOL at the semiannual meeting of the American Chemical Society.

Academics can work out techniques before they are ready for commercial investment. In-house efforts are often assembled on an as-needed basis, reflecting historical biases rather than optimal workflows.

Commercial software may be more optimized generically but is less well-suited to the idiosyncratic needs of individual pharmaceutical companies.

Among other issues, the interfaces between open-source software and other programs, or even interfaces with users, often require programming expertise beyond most so-called wet or bench scientists, or even bioinformaticists who have an expertise in programming but whose training is in bio-sciences.

Delano hopes his PyMOL can become a nucleus for advancing open-source efforts. All of the code is openly available; the company’s income comes from service contracts. It’s an unusual business model, he conceded. “When you’re starting from an ideological standpoint, you’ve got to be constrained by that.”

Next page: Low-cost molecular modeling.

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