Genetic Engineering & Biotechnology News says Philadelphia is great at landing federal research dollars. But turning research findings into viable treatments remains a relative weak spot.

"The two challenges for Philadelphia are getting the institutions to work more closely together and drawing more private venture capital," said GEN Senior News Editor Alex Philippides.

The new rankings are based on five factors: grants from the National Institutes of Health, venture capital funding, patents since 1976 including the word "biotechnology," lab space and jobs.

The San Francisco Bay Area came out in the top spot — with Boston (No. 2), suburban Washington, D.C. (No. 4) and New York City (No. 5) ranking as the top East Coast biopharma clusters.

Chris Molineaux, chief executive of Pennsylvania Bio, the trade association for the state's life sciences industry, isn't a fan of the ranking's methodology. He says the industry remains a major economic force.

"The rankings aside, Pennsylvania, and Philadelphia in particular, really are shaping the new face of the biopharma industry," Molineaux said.

Some 42,000 people work in the Philadelphia region's biopharma sector, according to a Select Greater Philadelphia report cited by GEN.

For the purposes of the list, "biopharma" includes both drug development and research into new treatments and technologies, Philippides said.

Regional competition for the biotech dollars remains fierce, even in the face of restructuring in the pharmaceutical industry in recent years. The sector tends to bring high-paying jobs. The challenge for Philadelphia, in terms of wooing investment, Philippides says, is standing out among a crowded field of East Coast markets.

"It takes more than just wishing to make it so," he said.